Well I have heard of others having this issue but I have never encountered it.
I would say make sure your files are not in other categories that are different from each other.
Example: A song/track/drop should not be in a MUSIC category and then in a PROMO category as only one of these will become the master category. A track can only have 1 SONG TYPE assigned to it.
Sometimes people move tracks around to different categories and when that happens the SONG TYPE of the track changes causes it to disappear in other categories that are not of the same TYPE.
In SAM you have the following SONG TYPES:
Music – S
Sound FX – X
Station ID – I
Jingles – J
Promos – P
Advertisements – A
News – N
Interviews – V
Other – C
When you move a track between those Main categories it will change the track to the associated category TYPE.
The track will still show up in the previous category until you click on the refresh icon at which time it will disappear.
Outside of that happening, I have no clue what else could be going on.