One common cause for the U3 to stop mining on your computer is SCREEN SAVER, or Auto POWER SAVER. Please try to disable the screen saver and the power saver on the computer you are mining with U3 and the cgminer.
Also, some USB3 ports may have some unstable power.
If it still doesn't work... Let us know.
I do not use a screen saver, I do not use any power saving modes, my computer does not sleep, I've disabled Windows from shutting off power to my USB ports. Believe me, I have done everything, above and beyond, to get two to work together, but it's not happening. It must be some fault with the units themselves, some sort of identical identification so my computer thinks they're both the same device or something; any other suggestions are welcomed.
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.
The list of potential causes already mentioned in this thread seem more likely.
I agree, they're no hotter running together or by themselves. I have exhausted the list of potential causes I believe, we need to come up with a new cause.