Ok, first, the 'windowed' mode greying out Resolution is by design, and logical.. If you are playing in a resizeable window, the game doesn't care what your resolution is - it just uses the dimensions of the window. The Resolution dropdown is for forcing a particular resolution in full screen only. It should be set to your monitor's maximum resolution by default.
I honestly don't know why EQ2 is bumping you out of full screen every time. If you change that setting from the launcher, it will do that the first time you log in, but it should save your settings after that and always start in your chosen mode. Oh.. there used to be an issue with saving configurations in Vista and sometimes Windows 7, IF you installed EQ2 in Program Files or Program Files (x86), but EQ2 should currently default to installing in Program Data, which fixes the problem.
You could try going to full screen mode (Alt-Enter is the toggle), then set the Resolution dropdown for your monitor's actual resolution, then go back to windowed mode. Exit the game to save everything, and start it again. If you don't know the monitor's resolution, you can find it in the Control Panel, or (easier) hit the Menu button on your monitor - most monitors will show you the current resolution.
Whatever you do, Do Not EVER click the Defaults button - That will change your monitor resolution, and screws up mouse synchronization, too (At least, thats what it does to me, and I'm not alone). If you do hit it by accident, hit ESCape and hope it goes back to normal.
If you're trying to play in a lower resolution than your monitor's maximum, but still be in a window, you'll have to set the monitor resolution manually in the Windows Control Panel (not in the game). The only reason to do this is if you want better frame rates in windowed mode at higher 'Quality' settings. I hate the lower quality 'performance' settings - EQ2 really doesn't degrade graphics settings gracefully. In fact I find it downright ugly. Not to mention its harder to see certain quest updates, harvests, and most important, Shinies! So I can see wanting to do this. Even a single step lower on the resolution slider can give your frame rates a big boost, and you don't really notice the resolution difference unless you're close to the screen.
Of course, changing the Windows resolution will move your desktop stuff around, so you'll want to consider carefully if you think you might do that.
As for the backup .ini files, they're all right there. It doesn't look like you have a problem with them, so no worries there. For reference, they are eq2.bik, eq2_recent, and bakupeq2...
Good luck.. I really hope something here helps.
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