I'm running mine out of seperate folders, so I'm no help there. The EQ2.ini only tells the game to either use default UIs or imported UIs {if you use stuff like EQ2Map or eq2interface}.

If it's not remembering game settings, the game may not be saving them. Try camping to character select and then exiting the game, or camping directly to desktop {depending on how you have been exiting the game}1 toon at a time. I saw someone recommending that to people who kept losing settings.

I was also losing settings across mine because even though Iset up IS to use 3 different folders, Launchpad wasn't. It would start out of the proper folder, but then Launchpad randomly started calling all 5 instances out of the same single folder. Worked fine until yesterday. Now I have to run from EverQuest2.exe instead of EQ2.exe to bypass the EQ2 launcher and get them all running from the proper locations.