Yeah, it could be that.
This is definitely past my level of knowledge. You've done everything possible software wise, so if you can it'd be a good idea to start playing around with BIOS settings to see if that changes things.
Now might also be a good time to contact SuperMicro support and ask them if there's anything special that needs to be done, for the IB adapter to work. (guessing you've scanned their manuals for that already?)