I may not have time to fully track down a couple of problems I have seen,
now that I have work arounds, so wanted to mention what I have seen in
case it helps someone else.
 A kernel with ACPI_PCI_FIXUP option set, when used on a Dell PowerEdge
has been setting links to irq 12 wich is the ps2 mouse irq. This would
cause a timeout on the ps2 mouse which would disable the controller,
which also disables the keyboard. The FIXUP option detected that the
links had not been set, and that the acpi table said they should be
at irq 12. I don't know if this is a bad acpi table, or a software error.
My ugly hack work around was to add code that would not set an irq if
it was irq 12.
  Another problem on a different Dell was a timeout on the audio driver
auich calibrate, using a GENERIC kerenel. I tracked this down to another
driver config line that when commented out allows the calibrate to complete.
The line is:
ahc0	at isa? port ? irq ?		# Adaptec 284x SCSI
It appears that this driver has not changed recently.
	Cliff Wright