One problem in older systems, is that resorces sharing doesn't work as well as it should, for the available IRQs. Older sytems (non-APIC) are generally limited to 4 IRQ's between all the PCI-class devices - this includes onboard devices and AGP
Finding 4 free IRQs for the PCI system is one issue, out of those potentially available, but normally 5, 9, 10, and 11 would be available on any system with no ISA cards in use - since an additional IRQ is often used, it may be worth disabling an unused serial or parallel port in BIOS, and specifiny the device as not existing in device manager.
The second case is that the slots often have an IRQ sharing relationship with onboard components, or with each other.
PCI SHOULD support IRQ sharing, but it is rather common for it to screw up!