Thank you for your replies. I finally had time to test a bit more.
swapping the cables:
The cables are fine, I switched them out with the same result.
swapping the inputs:
I can rule that out too, the problem is definitely the Stomp. Nothing else connected, directly into the interface, always the same result. The headphone output gives me a clean signal on both 1 and 2.
If it does end up being the output of the Stomp, have you tried cleaning it?
I did not, not sure how to go about that. But as I mentioned the problem has been there from the beginning so I do doubt that it would be that - seems like a software/firmware issue thing to me.
Other things I tried in the mean time:
Changing presets / resetting to factory settings / changing Output level (Inst / Line) / using different preset slots
So far nothing helped unfortunately..
What I did find out is that it only seems to happen (or become apparent) at a certain gain level. The higher, the more noticeable.
I bought the pedal new around September 2020 and encountered this issue in November that year already, when it unfortunately ruined a live session. I still have those recordings.
As I mentioned, just by comparing the sound waves it is very clearly visible how Output 2 is compressed or cut off at the higher side - the lower side looks identical.
I am attaching two more images I made with one of the factory presets. I used DIR: JazzRiver - I removed the stereo effects and added some gain to make it more clear.