The most common cause of reboots/controller swaps in the ATLAS is ethernet traffic. If it swaps back and forth between the two controllers than I don't believe the problem is one of them being bad. If that was the case it wouldn't cause a reboot when in "standby" mode.
What I suggest is disconnecting the ethernet cables from both controllers, and then visually monitoring them to see if it swaps controllers again. If it doesn't then you will need to see if you can put that ATLAS on it's own VLAN in order to isolate it from random ethernet traffic.
Hope this helps,
Since we haven't heard anything back from you, I'm going to mark this question as "assumed answered". If you have additional questions feel free to continue the discussion.