How many individual folders and possible locations are we talking about here? Maybe that's the reason Dolphin hangs.
Try keeping your folder structure clean with as less folders as possible.
For example I have it like this:
C:\Games\Video Games\Games\Wii
C:\Games\Video Games\Games\GC
With all the Wii ISOs in the Wii folder and all the GC .gcm files in the GC folder and not separate folders for every game.
Your problem could be because of to many folders and locations, but then again I could be wrong.
Try keeping your folder structure clean with as less folders as possible.
For example I have it like this:
C:\Games\Video Games\Games\Wii
C:\Games\Video Games\Games\GC
With all the Wii ISOs in the Wii folder and all the GC .gcm files in the GC folder and not separate folders for every game.
Your problem could be because of to many folders and locations, but then again I could be wrong.