i dont know tbh, just had a look at my stock music player, and it does look in other places for music, so i am not sure what to suggest really, also apparently if there is a period . infront of a folder name stock applications will disregard it.
can you not change the default save location of spotify to be the music folder.
found this in another post you could check your floder structure
Data Storage | Android Developers
Music/ - Media scanner classifies all media found here as user music.
Podcasts/ - Media scanner classifies all media found here as a podcast.
Ringtones/ - Media scanner classifies all media found here as a ringtone.
Alarms/ - Media scanner classifies all media found here as an alarm sound.
Notifications/ - Media scanner classifies all media found here as a notification sound.
Pictures/ - All photos (excluding those taken with the camera).
Movies/ - All movies (excluding those taken with the camcorder).
Download/ - Miscellaneous downloads.
if your tracks are in the right place then you could try clearing the data for the music player.
menu>settings>applications>manage applications>music>clear data, and then restart your phone ( long press power button )
and see if it rescans