Replying to myself here, just to add latest experiment.

I built a new kernel, with netbsd-4 source from last night, taking the
GENERIC.MP kernel and adding:
no acpi0 at mainbus

(I tried including both that line and the "no ioapic* at mainbus?" from
GENERIC.NOACPI, but it didn't seem to compile.)

So far this kernel seems to work OK. I tried to boot a GENERIC.MP built
from the same code, but it too gave re0: watchdog timeout errors after a
few minutes. So it would seem that my motherboard doesn't like acpi.

I guess I am now in a position where I could try a few things, so if anyone
would like to guide me, I'd be glad to offer my system for debugging this
issue.

-Lasse