> When I take my standard BIOS configuration and just disable APIC,
> then the problem disappears (both in 3.0 and -current).

Does your disk throughput suffer when you disable APIC in firmware?
(e.g. dd if=/dev/rwd0d of=/dev/null bs=... count=...)

> When I take my standard BIOS configuration and just disable SATA
> ports 3 and 4 (there are two SATA controllers in the nForce4) then
> the problem disappears (both in 3.0 and -current).

VERY interesting!  I have the opposite problem, sort of.

Back in early December, I added two additional SATA drives,
filling up the nf4's 4 SATA ports.  Somehow the firmware got
screwed up and appariently now only allows booting from one drive.
I had thought that the "load previous" option on the "advanced cmos"
page had fixed it, but it turned out that it didn't.  Fortunately
the one disk I can now boot from has grub on one of the partitions, and
grub *can* boot the other drives, so I at least have a kludge method
to boot the other drives.

In addition to this, NetBSD now gets the "lost interrupt" problem unless
I turn off APIC in the firmware.  (FreeBSD and Linux seem to be okay.)