Desktop becomes unresponsive during large file access

["Slim Joe" <slimjoe2k8@gmail.com>]

This is a problem that I've learned to live with since I first installed
a SATA hard disk. It afflicts two different systems, one running
Ubuntu and the other Debian.

When executing commands or programs  on large files (> 100 MB),
the system becomes unresponsive. Among such commands are:

(1) sha1sum -c dvdimage.sha1
(2) genisoimage dir/ > dvdimage.iso

By unresponsive, I mean it takes far much longer for subsequent
commands to execute. Iceweasel takes tens of seconds to pop
up. When I type text into a window even in a low-resource program
like vim, it takes several seconds before the text appears. The
system, in short, appears to hang, at least until the program
doing the large file access finishes execution.

Some info about my Debian installation:

Disk is a 500 GB hard drive found at /dev/sda.

$ lsmod | grep ata
ata_generic            10116  0
libata                165472  2 ata_generic,ahci
scsi_mod              160760  4 sg,sr_mod,sd_mod,libata
dock                   14112  1 libata

$ uname -srvm
Linux 2.6.26-1-amd64 #1 SMP Sat Nov 8 18:25:23 UTC 2008 x86_64

I suspect this is either a scheduling problem or a module conflict.
Is there some kernel magic or option I need to disable or enable to
make this problem go away? If I remember correctly, I didn't encounter
this problem when I was using PATA drives with DMA enabled.