Nick,
A thousand thanks for your thoughts and trying to dupe my issue -- it gave me incentive to try starting from scratch.
I moved the E1G42ET from an x8 slot to an x4 slot (the MBD-X9SCM-F-O has two of each), removed all other cards, reset bios settings to defaults, physically disabled the onboard nics, and did a fresh ESXi 5 install to a separate USB stick, and the E1G42ET worked! I added back the bios settings needed (primarily vt-d), the other cards, and re-enabled the onboard nics -- and it still works.
So from what I can determine the fix was either resetting bios settings or moving from an x8 slot to x4 slot (or the actual slot order). Theoretically the BIOS settings shouldn't be much different now than what they were before, but maybe there's something less obvious that was cleared by doing a "restore defaults".
When I can afford more down time I'd like to move the E1G42ET back to the x8 slot and see if it still works. If it does, I'll mark the reply that mentioned resetting the Supermicro bios settings as the "correct answer".
Thanks again,
-Dave