The most recent release announcements for libnds include a link to a working DeSmuME build. viewtopic.php?f=13&t=2389
This is an emulator problem, not a libnds problem. Please report the issue to the emulator authors and do not attempt to use old versions of libnds to avoid emulator bugs.
If you're using FAT to load files you could consider using nitroFS via libfilesystem instead. The latest builds work just fine with DeSmuME.