Hello:
First of all sorry for my english, I hope you untherstand me. I have the same problem than you and after I did the same things you did like change cables monitor, upgrede the Atem firmware to the latest one and the control software to 3.0 version I resolved the problem chaging the positiom on the rack of the Atem to the bottom of the rack where an air cooling machine blow directly to the Athem, them it is allways cold and works right, if you turn off the air and Atem turns warmer the problem returns. Seems very clear that the problem is the overheating! the real problem is that Atem have to work in a perfect cool embioramental that is not easy to get every where, I think that is a grave problem!!
I hope I help you.