Hi,
The problem is that the actual screen resolution used is different from the one you have configured (maybe because what you have configured isn't available). On Linux, the 'windowless full screen' option isn't actually available, and falls back to the normal full screen mode.
I've made a fix recently so the program checks the actual resolution, which will be in the next release. In the current release, Bridge Command is setting up the 2d view based on your manual configuration, but the 3d view based on the actual resolution.
In the short term, the easiest fix is for you to set the graphics_width and graphics_height to zero, so the resolution is automatically detected.
Please let me know if this resolves the issue.