Were you running steam at the time? Try closing steam first and trying again. I have experienced this as an issue when using heroic.
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I just tested it and unfortunately it did not fix the problem. Thing is, not Lutris nor Steam is picking up the gamepad. So I don't see Steam eating the input, since it also doesn't seem to recognize it.
Sorry, I misunderstood. What controller are you using? It seems odd that only jstest is detecting it. I initially needed to use an enviroment variable for my Steel series Stratus duo, but I think that was a layout issue.
I am really just using some very cheap off brand controller I found at some store. It does work on my RetroPie, but not my Debian pc. I have now switched over to my steam controller (since it works without any problems) and playing with it feels fine too.
So I guess I the problem has been solved for me, but the mystery of what causes this issue remains.
I'd suggest checking section 5.3 of the arch linux wiki gamepad page. Debian probably either has an older version of the related package or retroPie might have extra patches. Could not say what package for certain though. Arch Wiki Gamepad
Is it wireless? If so, and the controller supports it, try using it in wired mode. Sounds pointless, but have had issues with wireless controllers that worked fine when connected via USB.