Hello @UraniumDeer, are you still encountering this issue with an up to date system?
If you are, you should be able to set the SDL_VIDEO_MINIMIZE_ON_FOCUS_LOSS=0 env variable to avoid this behavior.
Closing pending feedback.
SDL_VIDEO_MINIMIZE_ON_FOCUS_LOSS=0x1 2017-04
HL minimizes(?) when you push CTRL, and "Show position of pointer when the Control key is pressed" in the "Mouse and Touchpad" settings.
OS: Ubuntu 12.04 LTS, 64 bit, nVidia 310.14 drivers
I tried replicating it in a couple of 3d games: