There is no way that Xastir can modify your xorg.conf. Something else
is doing it.

What you might want to try is to get back your working xorg.conf, and
save a back-up copy of it. Next time you experience the bizarre
change in resolution, check the modification time of xorg.conf and see
if you can figure out what you did at that time that could have caused
it. Then copy your backup xorg.conf back into place and see if that
still fixes the problem. If so, you need to figure out who's
scribbling into your xorg.conf and kill it dead.