Overheating issue
Forget case airflow right off the bat. With an open case it won't be a problem, and with a closed case it takes more than a few minutes to cause adverse effects, and you don't have enough components in there (power hungry video cards, etc.) to cause too much issues.
It could be a fan issue. If your fans are very silent at max speed, they might not go fast enough. But if they're relatively loud - which you seem to indicate, I wouldn't worry about them.
Knowledge is power: find out at what temperatures your CPU is when idle, and how fast and how much it climbs under load (and the delta between the idle/load). Run a temperature monitoring software like SpeedFan or Core Temp and come back to us with those readings.
According to Intel specs, the TCase max temperature is 77C. I'm not very familiar with TCase (whole CPU) vs TJunction (individual cores) temps on Xeons, but it seems that individual cores should probably not go above 77-5=72C. Allow a +/- 5C offset as well in software measurements. Further reading here.
Anyway, at first glance this does seem to be a badly seated heat sink.
Whenever you remove the CPU, use a little isopropyl alcohol to clean off any residue of thermal grease on both the top of CPU AND below the heat sink.
It might sound stupid, but make sure that no thin factory plastic film has been left on top of the CPU or below the heatsink, preventing metal-to-metal contact. This would wreak havoc.
Then apply a little bit thermal grease/paste/compound (very important!) and seat the heat sink carefully and tightly. If you're unsure how to apply it, read up on it: short article or longer article. Thermal paste isn't very expensive, so go with what seems good quality.
As mentioned in the short article, you could gently remove the heatsink immediately and check how well the the thermal paste has spread out, possibly helping you detect incorrect heat sink seating - not tight enough or even. After all, a bent heat sink bracket could be preventing proper contact. Don't hesitate to clean it up and start over.
Edit: I also agree with techie007's recommendation to upgrade BIOS/firmwares.
Update the BIOS and IPMI firmware for the motherboard, as they may be reporting a false overheat if the sensors aren't being recognized properly.
By doing this, and/or using their IPMI control utilities, you should be able to get the BMC updated and refreshed, so that it knows which sensors, fans, etc. are installed.
You can get them from SuperMicro's support site.
It may or may not matter, but what type of thermal grease are you using? if you aren't using any, that would explain the whole problem, but sometimes, thermal grease included with things just doesn't cut it. Try some Arctic Silver.