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Kernel bug?

I installed Etch a couple of weeks on a Toshiba Tecra A4-S211 for a friend of mine. Today I had to install some software and get his new printer working. While I was at it I ran apt-get update && apt-get upgrade. The kernel was patched during this upgrade and now the laptop will no longer shut down on its own. What follows are the last lines in the shut down messages, but even though the last line says "system halted" the monitor stays on and the laptop fails to power down. 

Deactivating swap...done.
Will now halt.
Sychronizing SCSI cache for disk sda:
System halted. This laptop has an ata hard drive in it, not SCSI or SATA, at least according to Toshiba's official documentation for this laptop. However, lspci identifies the hard drive controller as "00.1f.2 IDE Interface: Intel Corporation 82801FBM (ICH6M Sata Controller (rev 04)". There is also a bug during system startup which causes timeouts/hangs. The system has a problem identifying drives. This has been a problem since the initial Etch installation, although it has always shut down correctly up to now. 

Here is the relevant dmesg printout for what happens during boot:


PCI: Discovered primary peer bus 04 [IRQ]
PCI: Discovered primary peer bus 05 [IRQ]
PCI: Using IRQ router PIIX/ICH [8086/2641] at 0000:00:1f.0
PCI: setting IRQ 11 as level-triggered
PCI: Found IRQ 11 for device 0000:00:1f.2
PCI: Sharing IRQ 11 with 0000:00:1d.1
PCI: Found IRQ 11 for device 0000:06:06.0
PCI: Sharing IRQ 11 with 0000:00:1d.2
PCI: Sharing IRQ 11 with 0000:06:04.0
PCI: Sharing IRQ 11 with 0000:06:06.4
PCI: Cannot allocate resource region 0 of device 0000:06:06.0
PCI: Bridge: 0000:00:01.0
  IO window: c000-dfff
  MEM window: c0000000-cfffffff
  PREFETCH window: 90000000-9fffffff
PCI: Bridge: 0000:00:1c.0
  IO window: a000-bfff
  MEM window: bc000000-bfffffff
  PREFETCH window: 8c000000-8fffffff
PCI: Bridge: 0000:00:1c.1
  IO window: 8000-9fff
  MEM window: b8000000-bbffffff
  PREFETCH window: 88000000-8bffffff
PCI: Bus 7, cardbus bridge: 0000:06:06.0
  IO window: 00006000-000060ff
  IO window: 00006400-000064ff
  PREFETCH window: 80000000-81ffffff
  MEM window: b2000000-b3ffffff
PCI: Bridge: 0000:00:1e.0
  IO window: 6000-7fff
  MEM window: b0000000-b7ffffff
  PREFETCH window: 80000000-87ffffff
PCI: Found IRQ 11 for device 0000:00:01.0
PCI: Sharing IRQ 11 with 0000:00:1c.1
PCI: Sharing IRQ 11 with 0000:00:1d.3
PCI: Sharing IRQ 11 with 0000:01:00.0
PCI: Sharing IRQ 11 with 0000:02:00.0
PCI: Setting latency timer of device 0000:00:01.0 to 64
PCI: setting IRQ 10 as level-triggered
PCI: Found IRQ 10 for device 0000:00:1c.0
PCI: Sharing IRQ 10 with 0000:00:1e.2
PCI: Setting latency timer of device 0000:00:1c.0 to 64
PCI: Found IRQ 11 for device 0000:00:1c.1
PCI: Sharing IRQ 11 with 0000:00:01.0
PCI: Sharing IRQ 11 with 0000:00:1d.3
PCI: Sharing IRQ 11 with 0000:01:00.0
PCI: Sharing IRQ 11 with 0000:02:00.0
PCI: Setting latency timer of device 0000:00:1c.1 to 64
PCI: Setting latency timer of device 0000:00:1e.0 to 64
PCI: Found IRQ 11 for device 0000:06:06.0
PCI: Sharing IRQ 11 with 0000:00:1d.2
PCI: Sharing IRQ 11 with 0000:06:04.0
PCI: Sharing IRQ 11 with 0000:06:06.4
NET: Registered protocol family 2
IP route cache hash table entries: 4096 (order: 2, 16384 bytes)
TCP established hash table entries: 16384 (order: 5, 131072 bytes)
TCP bind hash table entries: 8192 (order: 4, 65536 bytes)
TCP: Hash tables configured (established 16384 bind 8192)
TCP reno registered
audit: initializing netlink socket (disabled)
audit(1176121167.776:1): initialized
VFS: Disk quotas dquot_6.5.1
Dquot-cache hash table entries: 1024 (order 0, 4096 bytes)
Initializing Cryptographic API
io scheduler noop registered
io scheduler anticipatory registered
io scheduler deadline registered
io scheduler cfq registered (default)
PCI: Setting latency timer of device 0000:00:01.0 to 64
assign_interrupt_mode Found MSI capability
Allocate Port Service[0000:00:01.0:pcie00]
PCI: Setting latency timer of device 0000:00:1c.0 to 64
assign_interrupt_mode Found MSI capability
Allocate Port Service[0000:00:1c.0:pcie00]
Allocate Port Service[0000:00:1c.0:pcie02]
PCI: Setting latency timer of device 0000:00:1c.1 to 64
assign_interrupt_mode Found MSI capability
Allocate Port Service[0000:00:1c.1:pcie00]
Allocate Port Service[0000:00:1c.1:pcie02]
isapnp: Scanning for PnP cards...
isapnp: No Plug & Play device found
Serial: 8250/16550 driver $Revision: 1.90 $ 4 ports, IRQ sharing enabled
serial8250: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A
PCI: setting IRQ 5 as level-triggered
PCI: Found IRQ 5 for device 0000:00:1e.3
PCI: Sharing IRQ 5 with 0000:06:06.3
RAMDISK driver initialized: 16 RAM disks of 8192K size 1024 blocksize
PNP: No PS/2 controller found. Probing ports directly.
i8042.c: Detected active multiplexing controller, rev 1.1.
serio: i8042 AUX0 port at 0x60,0x64 irq 12
serio: i8042 AUX1 port at 0x60,0x64 irq 12
serio: i8042 AUX2 port at 0x60,0x64 irq 12
serio: i8042 AUX3 port at 0x60,0x64 irq 12
serio: i8042 KBD port at 0x60,0x64 irq 1
mice: PS/2 mouse device common for all mice
TCP bic registered
NET: Registered protocol family 1
NET: Registered protocol family 17
NET: Registered protocol family 8
NET: Registered protocol family 20
Using IPI No-Shortcut mode
Freeing unused kernel memory: 196k freed
Time: tsc clocksource has been installed.
input: AT Translated Set 2 keyboard as /class/input/input0
usbcore: registered new driver usbfs
usbcore: registered new driver hub
USB Universal Host Controller Interface driver v3.0
PCI: Found IRQ 11 for device 0000:00:1d.0
PCI: Sharing IRQ 11 with 0000:00:1d.7
PCI: Setting latency timer of device 0000:00:1d.0 to 64
uhci_hcd 0000:00:1d.0: UHCI Host Controller
uhci_hcd 0000:00:1d.0: new USB bus registered, assigned bus number 1
uhci_hcd 0000:00:1d.0: irq 11, io base 0x00001200
usb usb1: configuration #1 chosen from 1 choice
hub 1-0:1.0: USB hub found
hub 1-0:1.0: 2 ports detected
Uniform Multi-Platform E-IDE driver Revision: 7.00alpha2
ide: Assuming 33MHz system bus speed for PIO modes; override with idebus=xx 
PCI: Found IRQ 11 for device 0000:00:1d.1
PCI: Sharing IRQ 11 with 0000:00:1f.2
PCI: Setting latency timer of device 0000:00:1d.1 to 64
uhci_hcd 0000:00:1d.1: UHCI Host Controller
uhci_hcd 0000:00:1d.1: new USB bus registered, assigned bus number 2
uhci_hcd 0000:00:1d.1: irq 11, io base 0x00001220
usb usb2: configuration #1 chosen from 1 choice
hub 2-0:1.0: USB hub found
hub 2-0:1.0: 2 ports detected
ieee1394: Initialized config rom entry `ip1394'
PCI: Found IRQ 11 for device 0000:00:1d.2
PCI: Sharing IRQ 11 with 0000:06:04.0
PCI: Sharing IRQ 11 with 0000:06:06.0
PCI: Sharing IRQ 11 with 0000:06:06.4
PCI: Setting latency timer of device 0000:00:1d.2 to 64
uhci_hcd 0000:00:1d.2: UHCI Host Controller
uhci_hcd 0000:00:1d.2: new USB bus registered, assigned bus number 3
uhci_hcd 0000:00:1d.2: irq 11, io base 0x00001240
usb usb3: configuration #1 chosen from 1 choice
hub 3-0:1.0: USB hub found
hub 3-0:1.0: 2 ports detected
PCI: Found IRQ 11 for device 0000:00:1d.3
PCI: Sharing IRQ 11 with 0000:01:00.0
PCI: Sharing IRQ 11 with 0000:02:00.0
PCI: Setting latency timer of device 0000:00:1d.3 to 64
uhci_hcd 0000:00:1d.3: UHCI Host Controller
uhci_hcd 0000:00:1d.3: new USB bus registered, assigned bus number 4
uhci_hcd 0000:00:1d.3: irq 11, io base 0x00001260
usb usb4: configuration #1 chosen from 1 choice
hub 4-0:1.0: USB hub found
hub 4-0:1.0: 2 ports detected
PCI: Enabling device 0000:00:1d.7 (0000 -> 0002)
PCI: Found IRQ 11 for device 0000:00:1d.7
PCI: Sharing IRQ 11 with 0000:00:1d.0
PCI: Setting latency timer of device 0000:00:1d.7 to 64
ehci_hcd 0000:00:1d.7: EHCI Host Controller
ehci_hcd 0000:00:1d.7: new USB bus registered, assigned bus number 5
ehci_hcd 0000:00:1d.7: debug port 1
PCI: cache line size of 32 is not supported by device 0000:00:1d.7
ehci_hcd 0000:00:1d.7: irq 11, io mem 0xf4000000
ehci_hcd 0000:00:1d.7: USB 2.0 started, EHCI 1.00, driver 10 Dec 2004
usb usb5: configuration #1 chosen from 1 choice
hub 5-0:1.0: USB hub found
hub 5-0:1.0: 8 ports detected
PCI: Found IRQ 11 for device 0000:06:06.2
ohci1394: fw-host0: OHCI-1394 1.1 (PCI): IRQ=[11] MMIO=[b0000000-b00007ff] Max Packet=[2048] IR/IT contexts=[4/8] 
SCSI subsystem initialized
libata version 2.00 loaded.
ahci 0000:00:1f.2: version 2.0
PCI: Found IRQ 11 for device 0000:00:1f.2
PCI: Sharing IRQ 11 with 0000:00:1d.1
ahci: probe of 0000:00:1f.2 failed with error -12
ata_piix 0000:00:1f.2: version 2.00
ata_piix 0000:00:1f.2: MAP [ P0 P2 IDE IDE ]
PCI: Enabling device 0000:00:1f.2 (0000 -> 0001)
PCI: Found IRQ 11 for device 0000:00:1f.2
PCI: Sharing IRQ 11 with 0000:00:1d.1
PCI: Setting latency timer of device 0000:00:1f.2 to 64
ata1: SATA max UDMA/133 cmd 0x1F0 ctl 0x3F6 bmdma 0x1100 irq 14
scsi0 : ata_piix
ata1.00: ATA-6, max UDMA/100, 117210240 sectors: LBA48
ata1.00: ata1: dev 0 multi count 16
ata1.00: applying bridge limits
ata1.00: configured for UDMA/100
  Vendor: ATA       Model: IC25N060ATMR04-0  Rev: MO3O
  Type:   Direct-Access                      ANSI SCSI revision: 05
ata2: PATA max UDMA/100 cmd 0x170 ctl 0x376 bmdma 0x1108 irq 15
When the boot process reaches the above line it hangs for about a minute and then continues although there are hangs of similar lengths at each qc timeout below. 
scsi1 : ata_piix
ata2.00: ATAPI, max UDMA/33
ieee1394: Host added: ID:BUS[0-00:1023]  GUID[00080da0d1bca69f]
ata2.01: qc timeout (cmd 0xa1)
ata2.01: failed to IDENTIFY (I/O error, err_mask=0x4)
ata2: failed to recover some devices, retrying in 5 secs
ata2.01: qc timeout (cmd 0xa1)
ata2.01: failed to IDENTIFY (I/O error, err_mask=0x4)
ata2: failed to recover some devices, retrying in 5 secs
ata2.01: qc timeout (cmd 0xa1)
ata2.01: failed to IDENTIFY (I/O error, err_mask=0x4)
ata2: failed to recover some devices, retrying in 5 secs
ata2.00: configured for UDMA/33
  Vendor: MATSHITA  Model: UJDA750 DVD/CDRW  Rev: 1.60
  Type:   CD-ROM                             ANSI SCSI revision: 05
SCSI device sda: 117210240 512-byte hdwr sectors (60012 MB)
sda: Write Protect is off
sda: Mode Sense: 00 3a 00 00
SCSI device sda: drive cache: write back
SCSI device sda: 117210240 512-byte hdwr sectors (60012 MB)
sda: Write Protect is off
sda: Mode Sense: 00 3a 00 00
SCSI device sda: drive cache: write back
 sda: sda1 sda2 < sda5 >
sd 0:0:0:0: Attached scsi disk sda
Attempting manual resume
ReiserFS: sda1: found reiserfs format "3.6" with standard journal
ReiserFS: sda1: using ordered data mode
ReiserFS: sda1: journal params: device sda1, size 8192, journal first block 18, max trans len 1024, max batch 900, max commit age 30, max trans age 30 
ReiserFS: sda1: checking transaction log (sda1)
ReiserFS: sda1: Using r5 hash to sort names
I looked in kern.log and syslog and found nothing of any more detail than what is in dmesg.
Anyone know what is going on here?
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