Display resolution settings not storing since upgrading monitors

We have (2) Mac Pros and since upgrading to larger monitors we have been having issues with the resolution settings not "storing" in display preferences. The computer setups are slightly different, and the monitor sizes and make/models are both different, but the problems are the same:

1) Mac Pro DVI out > VGA switcher > Monitor VGA input

2) Mac Pro DVI out > VGA switcher > DVI switcher > Monitor DVI input

(*Note - I know this whole setup seems ridiculous, but it's the way each of the rooms were hard-wired)

With both machines the problems intermittently vary from the resolution itself changing at random when turning on the machine each day, to the desktop background being about 2/3 the size of the screen, while all of the icons and rest of the desktop being normal sized/extended to the edges of the monitor as it should.

It seems that if we change resolution to anything else, and then change back to the desired resolution, that usually solves the problem.

Does anyone know why these settings won't save?

(*Note - we recently upgraded to Lion, but the issue was there before and after the upgrade.)