When Cxbx-Reloaded is build with the DEBUG (as opposed to the default RELEASE) configuration, the main window size is smaller. (That, or the window size is larger under RELEASE builds.)
In any case, for this issue:
I haven't been able to reproduce this, I built two binaries: one in release configuration and the other in debug, but they appear to be the same size.

This is an old issue, is the issue still exist?
I believe this has been fixes months ago when resize-window functionality was added