Just to bring the list up to date, I went onsite, popped the case
open, and guess what I saw..
SUPER X5DP8-G2 REV 1.2
rather than X5DL8-GG, so it looks like the vendor pulled a fast
one. spec sheet on that lists onboard Intel 82546EB dual port GigE,
but note that I've already got one single port Pro/1000XT and one
dual port Pro/1000MT in there, so I should've been seeing 5 em
rather than 3. Turned out the MT was the one that was hiding, but
after a bit more testing, I managed to get everything to appear by
turning down the first 3 PCI slots to 33mhz from 133, 100, 100. I
then set speed back to auto, it autosensed 133, 100, 100, and
everything showed up again. Did a few more reboots, and it seems to
be OK.