neo, I had the EXACT same problem.. here was my situation (it's still not really resolved btw):
I have 2 ISA slots, 5 PCI slots, and 1 AGP slot. I have a video card in the AGP, I used to have a 2nd video card in the PCI #1 (it didn't work when I tried changing drivers, I'll have to try it again when I reinstall windows), I have a soundcard in PCI #2, I have a ATA66 card in PCI #3, a Hollywood + in PCI#4 and a PCI hardware 3com modem in PCI #5.
my problem was this. the Hollywood + was sharing an irq with the modem, and whenever I tried to do anything on the modem while playing a DVD, it gave me a blue screen, or it just simply hardlocked.
I then tried to change IRQ's. I found that isn't possible (even with the BIOS allowing PnP OS etc, and having Automatic settings off in windows). the computer wouldn't let me change IRQ's at all.
I then found out that the problem really was one of busmastered slots. ie, the Hollywood + and Modem were sharing a busmaster, and therefor had to have the same IRQ. I also found out that my Video cards were both sharing a busmaster as well (same story, AGP and PCI#1 share an IRQ).
my video cards worked absolutely FINE until I tried updating drivers. the computer simply wouldn't start up with the second video card.
recently I've tried to see if ACPI is available in 98, however no matter what I did, it didn't seem to change anything (in terms of IRQ's), HOWEVER for some reason, all of the sudden, I am able to use both at a time.. try going into the system properties/device manager/system devices/PCI bus.. take a look in there for something to do with ACPI (that's all I changed).