devkitPro

When the docs say you can initialize the sounbank from the filesystem, what filesystem is meant?

GBFS?
NDS?
Stored on the ROM directly?

I had this same problem on my machine and tracked it down, sounds different than your problem but perhaps this will help others

I had an environment variable defined GCC_EXEC_PREFIX that pointed at a no-longer existing directory. I deleted the variable and everything started working.