In Wayland, when I'm switching to a Webbrowser to write a forum post, for example, and back to SK, I see the game for like a second and then it immediately logs me out. It's running fine in the background, but as soon as it gets the focus back, I get the login screen.
It would be helpful if you send over your projectx.log so we can take a look. You can either paste it here or email it to support@spiralknights.com.
Similarly, please make sure you are filing a /bug report in game when you can. I realize you can't for this issue since you're being booted.