I was using the latest stable version on the desmume website.What Desmume version are you using? Get the latest build on here!
https://ci.appveyor.com/project/zeromus/desmume/build/artifacts
Select JOBS, then x86 (32 bit) or x64 (64 bit) and select ARTIFACTS. Finally select file to download it.
Most importantly, delete DESMUME.INI file from C:\Desmume folder (or anything).
Any other bugs, please visit Desmume forum here! http://forums.desmume.org/
Anyway, enjoy the games! 