Kerbal Space Program

I cannot find the exact sequence of steps to reproduce the bug, but the general idea is:

1. In whatever way that is available (from the menu / the launcher / by editing settings.cfg right after installing the game and before it writes to ~/.config/unity3d / by editing both settings.cfg and prefs under ~/.config/unity3d) change the graphics mode to windowed. I also change the resolution to 1440x900, but the bug can also be reproduced with seemingly no difference at 1280x720.
2. Launch the game through Steam (it seems more likely to pop up compared to launching as ./KSP.x86_64)
3. Wait until the initial black window disappears and the "loading" window appears
4. Move the window. This can be done both during the loading and from the menu, there seems to be no difference. The bug also sometimes happens without any window movement.

Result: window size (and resolution) change. Most often to one of two resolutions:

1. 1440x29
2. [huge number around 55000]x29

Occasionally I also see 1440x0 and [55xxx]x0. I have seen 31400x0 and 100x100, each of them once. I have also seen many times the "loading" window disappear completely, with the process still running (I killed it with SIGTERM). The first attachment contains Player.log for this particular failure path. It doesn't seem particularly informative, though.

The second attachment contains a log of the loading sequence where multiple seemingly random resizes were requested: first to 5036x900, then to 1716x900. When the game loaded and I was dropped in the menu, the settings dialog said that the resolution was "custom". I was not moving the window during this run at all.

It seems that when I move the window during loading and it resizes, no traces are left in Player.log, but when I do the same from the main menu, entries like this one get written to Player.log:

requesting resize 1440 x 900
resizing window to 1440 x 900
Desktop is 1920 x 1080 @ 60 Hz
[MessageSystem] Reposition 34.91556 37606

So the game thinks it restores the old resolution, but actually the new resolution that gets set is 1440x29.

The bug can be reproduced around 3/4 of the time. I don't see any fixed pattern. I don't see any way to control the new erroneous resolution.

The game version is 1.2.2 from Steam and I'm under the latest Manjaro Linux.

How can I reset the game's settings entirely to make sure that I'm running a clean test? I.e., is there ANY state whatsoever that is stored outside of steamapps/ and ~/.config/unity3d?