the only time I've ever had this issue (ages back) was when I had a mod enabled that used it's own custom music (as in lua controlling the musicmanager, not just ogg replacements) without using the soundtrack menu or music API

basically one mod sees you're in whatever floor/room, checks if the game is playing music A, it's not, so music A starts, second mod sees you're in floor/room, checks if game is playing music B, it's not since it's playing A, so music B is started, then you move to a new room and the first mod checks for music A again, but music B is playing, so start music A, second mod checks for music B, etc etc repeat every time you change rooms

if its not a conflict of another mod trying to control music then I don't have any idea why this would happen

had someone comment on the soundtrack menu about having this issue and then it stopped after they re-downloaded a fresh copy of the mod, so yeah, might just be a corrupt or not up-to-date file issue

so if you get this problem try deleting your music callback and soundtrack menu mods and letting steam download a new copy

I addressed a solution to this issue when it is caused by Antibirth++ in the discussion "Antibirth+++ and All Antibirth Jingles compatibility".