The puzzle is now solved!
The INPUT 1 jack must be a high-impedance instrument-only input, I was using a JACK-JACK cable.
I've tried using the XLR connector, and now you do get a decent response. Not as good as INPUT 3, but it makes sense!
Be careful using INPUT 1 XLR, as line input, because if we press phantom power we can cause a problem.
If you read the manual, I don't think it says anywhere that inputs 1-2 are supposed to be used as line inputs only if using XLR connectors. In fact, it says the exact opposite on page 17:
I'd say it's actually more likely that people will want to use phone plugs to connect line level devices than XLR, and the XLR inputs are more likely to be only used for microphones. So phone plug inputs on the combo connectors really should work just as well or better than XLR for line level sources.
I'll try some tests on my own unit when I get back home so next weekend at the soonest.
Occasionally I'd love having line inputs with gain that doesn't need to be applied in software and besides the device was always marketed as having 4 instead of 2 line inputs anyway. If there really is some kind of a design error here, I wonder what to do? There's still plenty of the warranty period left in case I'd try to get it exchanged, but are there even any revisions which don't have a problem? I do like the unit otherwise.
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