Just for kicks, try a different music player. Winamp is good and you can also try the 2 week PowerAmp trial. Try to clear any playlists or anything from the stock app and don't even touch it, see if that helps at all.
Tried another music player - same result. When the phone rings, I get a screen for an app called DLNA and it wants to know if I want to share files and music starts playing at the same time. If I cancel the DLNA app (which I've never used) , the music continues to play during the phone call unless I go to the music app and hit pause. I tried to remove rhe DLNA app, but there's no way to uninstall it.