There's 2 possible files as I mentioned. autoexec.cfg isn't always there (this depends on your setup). There's also config.cfg which by default IS present.
Xonotic loads autoexec.cfg if it exists, then it loads config.cfg.
In the config files you can bind keys to other meanings than their default.
Notes:
- They're *.cfg files, not *.config files. The game only uses files ending in *.cfg (usually).
- The only other thing is to check you haven't enabled some different keyboard map in Ubuntu when launching the game. I know it's possible but never done it myself.
Edited to add:
Re-reading your first post, do you mean that this happens WITHIN Xon, or that after you've run (and quit) Xon, that this happens in a terminal/Xterm?
If it's happening in the terminal, then you might want to look into the terminal settings to check the enabled options. Some terminals (eg: Gnome Terminal) have menu options and an option to "reset" or "reset and clear" the terminal which might help too.
You might also be activating the Ubuntu equivalent of Window's "Sticky Keys" while in Xon playing a game (which would make Ubuntu think a key is stuck down). You'd need to look through your Ubuntu settings to see if that's enabled or how to turn it off.
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