I am having the exact same problem. Other versions of Zsnexbox worked perfectly, however no matter what I name my path, the roms don't show up.
CODE
F:\Roms\Snes\Roms
SavePartition=E
And my roms are in that dir as it worked on all the prior versions :-|
Anyway, with this little hickup aside, FANTASTIC version. Love the cheat code database. That really made my day

Actually, now that I think about it, I think I disabled the path loading when testing the new rom browser (and then forgot to re-enale it because I allways put my roms in D:\roms). So it will only scan the D:\roms on startup. But you can still browse to anywhere the ROMs actually are if they are not in this folder.
I'll make a new release later today maybe with this path loading bug fixed.