If you have two AntMiner U3's where they both work fine on their own, I cannot imagine how thermal management would have anything to do with them not working fine when both are plugged in - unless both were put into an enclosed box together significantly raising each other's temps. Given the thermal mass involved, even that scenario seems unlikely to throw errors practically immediately.
It's not a "thermal management" issue. There are dielectric effects of having excess paste covering CCA components that should not be covered. I didn't believe it either but the results are real.
What results do you speak of? Did you have more than one U3 that wouldn't run together, then you cleaned up the paste, then they ran together just fine? If they work just fine by themselves, how could excess thermal paste cause any issue when they're running together? There are a few people who posted that they were able to run more than one U3 at a time, that was right after ck updated cgminer. Maybe I need to try an older 4.8.x version? Or maybe it's just my computers don't agree with more than one U3? I don't know why it would work for some, but not for me.