Late reply but may be helpful to others:
Don't put "too" many ROMs of the wrong extension into any folder. The A320 has this concept of a "juikebox" which checks the filesystem for "known file types.
These extensions are governed by emulators which are configured to be the default program associated with the extension.
Off hand, I think I made the extensions .A26 for vAtari, so all ROMs should have this extension. Also, they should not be compressed.
Another possible issue I found was having "too many" ROMs in the one directory - there may be an internal operating system limit on this. I wouldn't put more than 100 or so in one directory. Create multiple directories if required.
ie. Atari-A, Atari-B, Atari-C and so on, one for each letter of the alphabet.