Dolphin stopped saving controller settings!

[Alphaeus]

So for the past few weeks Dolphin as been working great for the most part. I use 360 controllers via USB. Then today while trying to setup controllers for a third player for Brawl the controls went all funky (my joystick now controls both player 1 and 2) and nothing in the controller settings allows me to change it. Even if I clear it, start over, or don't load any controller in the settings games will launch with the messed up configuration.

I tried reinstalling Dolphin to another location and while I was able to get most of the controls back, I'm currently unable to edit them. Why can't I edit my controller settings!? Switching USB ports, restarting my computer...nothing works.

All I want is for the controller settings to save properly. Is there a place where controller cache is stored that I should delete or something?

Thanks in advanced.

[HawaiianPunch]

Is Dolphin in a protected folder (get it out of "Program Files")? Right click the Dolphin folder, click properties and make sure read only is not checked.