Starting from ezQuake version 1.8 you don't need commandline switches anymore. There's an upgrading part on the ezQuake docs page that people never seem to read and they still use +cfg_load on the cmdline, which can cause some problems, especially when initializing input.

The variables you might want to check after removing cmdline options are:

/ruleset smackdown

/in_mouse 1,2 or 3 (2 for dinput, 3 for raw input)

/allow_scripts 2

/vid_mode (use -1 for custom resolutions in combination with vid_customheight/width).

/vid_displayfrequency