what resets exactly?

if its g_gametype and fraglimit it might be that you have rotation.txt messing up with your server rotation in your server cfg file.

i have the same problem.
i solved it by making seperate cfg file named cfg.txt
then when i enter the game i just do /exec cfg.txt in console.

the reason settings dissapear is because quake uses more then 1
cfg file. every mod or gametype has its own cfg. if you change the
settings quake stores it, but at quake startup it loads the old cfg again.

make sure that the cfg in excessiveplus and baseq3 are the same.
then your problem must be solved. until you change settings again....