Yeah, I think it is the other way around. Not a big deal, that, though it can be the source of some confusion. Database rebuilds look for non-subdir'd files first, then for the subdirectory versions. At playback time, the player looks into the subdirectories first, and then for the flat file versions. I think.
Rather than theoretically "fixing" that someday, I would very much prefer that a future release of the player software merely include code to automatically write new FIDS to the subdirectories when uploading. Unconditionally would be fine, but one could gate it by requiring that at least one subdir already exists or that the player be empty.
I have modified Hijack-v344 to automatically redirect ALL acceseses to the subdirs, player or otherwise, but only when performed through the symlinks in /empeg/fids?/ (not when done via /drive?/fids/, but only if at least one (any) subdir already exists. I didn't bother with the "empty player" case. To be released soon.
Cheers