I think I figured out why it happens.
I suspect it's libnotify, for example when you're listening to music and your track changes. That causes the notification to appear, and in combination with Compiz this "de-fullscreenizes" Spring into windowed mode.
The working workaround for this is to disable Compiz before running Spring.
Just thought I'd share this for those who are also struggling with this problem.
Spring jumps into windowed mode
Moderator: Moderators
Re: Spring jumps into windowed mode
compositing on linux has a history of breaking spring in interesting ways, it's best to disable it anyway. it's also a good idea to play spring in a fullscreen window instead of native fullscreen.