Nevermind, figured it out myself after a few hours of fiddling.
It would be good forum etiquette to post what you did to get the issue resolved. That way anyone with a similar problem would come across this and see the resolution.
Fair enough, it wasn't really much of a solution as I don't think it was a problem with my method to begin with.
I changed the storage path to the [device name]\card\ and then just left it like that for a bit and restarted Musicbee. Afterwards it seemed to work fine.
(Don't know why I didn't try just leaving it as is before really, I guess I figured I was doing something wrong so I didn't think of just trying the same thing but again.)