Just to clarify. You are generating your libraries separately, first videos, then music, right? And you are generating the libraries only on the sub folders, not the top directory? Also, you are generating and not updating, correct?
EX:
MUSIC <don’t point any directories here to build.
VIDEOS <point video directory here.
VIDEO 1
VIDEO 2
(Etc)
MUSIC <point music directory here.
SONG 1
SONG 2
(Etc)