Obviously we are having trouble duplicating your problem. This is probably because you are doing something that we are not, or vice versa.
With this in mind, could you do a "clear setup", and then give a step by step description of the simplest possible route to demonstrate the problem. Like you, I think that this is probably a software issue, but unless we can see it we can't help.
I'm puzzled that above you say you use TRS cables, whereas before you referred to mono cables, which to my mind are TS.