Oops, I just hit the "Suggest as answer" button on danut's last post, thinking I was hitting "Suggest an anser." Apologies.
First of all, I need to ask a simple question, only because I was having a volume boost issue with my timefactor and solved it. You have your input and output jacks set to guitar>amp or line>line, right? Once when I was updating the TF software, I bumped the input switch without knowing it, and I wound up blaming the software.
But from what you're describing, I don't think this is the case.
I suspect a hardware issue, personally. It's possible that just your output B is refusing to switch from line to guitar level or vice versa. A lot of times a toggle switch will have a short across two leads that effectively lock it in one state or another. I fixed this on two pedals yesterday. Or it could be something wrong with the switching in the TRS output jack. It's tough to say though without a schematic in front of me, so if it's a really bad problem, which it sounds like it is, I'd say send it in to Eventide. I can't immagine what you're describing can be software or user error.
