
What you are experiencing is a display driver that is capable of rotating the desktop. The initial display startup will choose what it thinks is the "best" fullscreen mode, which is normally the one at the end of the mode list. So you are getting something like 800 x 1280 instead of 1280 x 800 as your video mode.
I had noticed this a while back, and had taken a note that it was something I needed to fix, but never did get round to doing it.
For now the fix is to just select a different video mode (you may need to turn either your monitor or your head sideways to do this

Bakers point holds true, by the way. While I believe this engine is mostly good enough for some general ID1 play, I don't recommend it for use as a more general purpose Quake client. Switching to C++ and Direct3D are two huge leaps into the unknown for Quake, either of which could bring in all manner of unknown problems. Step 1 is always to see if any issues with it also occur in regular Win/GL Quake.