Isn't that normal behavior in RPG Maker?
Viewing post in Post-battle skip?
Not in my experience.
Well, there may be one way that I haven't tested. The engine gets weird about music start points if you don't play at 100 pitch; I have warnings about that in the description about this very plugin. (And I don't know how to fix that; it's a problem with the engine, not my plugin.) Are you playing the overworld music at a pitch value other than 100?
EDIT: The music still picked up where it left off for me even when I set the pitch to 120. Sorry, what you describe doesn't happen for me at all.