To clarify, are you playing on 1.0.5, or 1.0.6? Old 1.0.6 vs the one I just uploaded shouldn't have effected this in any way. Testing it out just now, it seems like the music does indeed resume correctly after the battle as far as I can tell.
Alright. Yeah, I'm going to chalk that one up to RPGMaker being odd for now then, but I appreciate the report. Let me know if it happens again, or you see something similar.
