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linux-kernel-2.4.27, hpt366 ide channel not detected

I have two extra IDE [RAID] channels on my motherboard that use the hpt366 driver and I am using as just regular IDE channels. There is just one hard drive that is the master on the first of these channels which has several data partitions. With linux-kernel 2.4.25 with debian patches built with make-kpkg, I get messages like: 

Sep  3 12:36:25 localhost kernel: HPT372: IDE controller at PCI slot 00:13.0
Sep  3 12:36:25 localhost kernel: HPT372: chipset revision 5
Sep 3 12:36:25 localhost kernel: HPT372: not 100%% native mode: will probe irqs later 
Sep  3 12:36:25 localhost kernel: HPT37X: using 33MHz PCI clock
Sep 3 12:36:25 localhost kernel: ide2: BM-DMA at 0xc000-0xc007, BIOS settings: hde:DMA, hdf:pio Sep 3 12:36:25 localhost kernel: ide3: BM-DMA at 0xc008-0xc00f, BIOS settings: hdg:pio, hdh:pio
and everything works fine. But with 2.4.27, both make-kpkg built and kernel-image-2.4.27-1-k7, I get nothing. It's like it is not even there. I don't even really know where to start troubleshooting. scanpci lists: 
pci bus 0x0000 cardnum 0x13 function 0x00: vendor 0x1103 device 0x0004
 Triones Technologies, Inc. HPT366/368/370/370A/372
so at least that much is still getting detected. And cat /proc/pci lists:
  Bus  0, device  19, function  0:
RAID bus controller: Triones Technologies, Inc. HPT366/368/370/370A/372 (rev 5). 
      IRQ 10.
      Master Capable.  Latency=64.  Min Gnt=8.Max Lat=8.
      I/O at 0xb000 [0xb007].
      I/O at 0xb400 [0xb403].
      I/O at 0xb800 [0xb807].
      I/O at 0xbc00 [0xbc03].
      I/O at 0xc000 [0xc0ff].
Manually modprobing/adding to /etc/modules hpt366 results in it getting loaded with no apparent errors, but otherwise doesn't seem to help.
The 2 'normal' ide channels still work and the system as far as I can tell has no other problems.
Any ideas? Is it related to Message-ID: <20040823100156.GA1380@uniflux-line.net>? Though that poster didn't seem to get any answers as well.

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