That's strange, just to be sure, by Green Mode we are talking about this?
If that's the case when opening the game during the BolHut animation at startup, if you hold R and then press L on keyboard, you change the shader. With gamepad it would be the R shoulder and the L shoulder. It's a hidden easter egg.
Something has to be triggering this on startup unintentionally, check for any devices/controllers connected that might be causing this.
I just uploaded a new version of the game for Windows (cannot access Linux right now) where you have to press R+L+A at the same time hopefully it fixes the issue, please download and try it.