Did you ever restripe your drives when you went to 10.4? Its a good idea to do so as Apple made a lot of changes with they way they work with SCSI between 10.3. and 10.4.
if its a vincent 601 card and you’re running 8.2 there should be a little check box in the hardware preferences
enable 601 or 720 or something like that.
Dah King
Its also worth-while to check your energy saver control panel to make sure that “put the hard disk(s) to sleep when possible” is not turned on. If it happens after about 20 minutes that’s what it sounds like.