I had a problem similar to that actually, just like SonicBrawler said, formating the sd card could be the solution... and I know that this is obvious, be sure to check if your sd card is not locked, or that it locks itself when entering the wii.
If those are not the problem, check this:
"Important:
1. Folders can only be swapped with special combination buttons at the 1st controller.
2. You need a regular SD card. 2GB is the max size.
3. Default folder at startup is RSB4.
4. You can use any controllers at any ports just make sure that the code you are using coincides with the controller you have in the first port."
I found this information in this thread:
http://forums.kc-mm.com/index.php?topic=51912.210You should ask for help there! Mr.MW would help you with this since this is his work
