Yeah, three things just to be sure.
First after any nandroid restore or new flash, go to TWRP, Wipe, Advanced and wipe cache and Dalvik.
If that doesn't fix it, your media database is confused. It's neither rare nor common, just happens sometimes - even if you're not rooted.
To fix, go to main settings, Apps, All and find Media Storage - you should have maybe a few tens of MB of data. Clear cache and data, reboot phone and leave it alone for fifteen to twenty minutes - that database will rebuild itself in its own time.
You will have to probably reset your ringtone preferences, alarms and so forth.
If it's still broken (and give it time to be sure) copy off all of your personal music files and then delete them. Add them back one at a time.
Amazingly, this is rare but known - an mp3 file gets corrupted (no one I know has figured out how) and it plays heck with all media handling and file storage.
I suppose in theory that any file could get corrupted but I've only seen it with music files, usually mp3 files.
Hope this helps!