Sorry to say, same problem here.
So far its only at the main menu for me and yes, it does seem to be when the loop restarts. If you go to options and toggle music off and on again, it stops until the loop restarts again. Hmmm...
A small problem which I'm sure will be worked out, right? It is an annoying blemish to such a fine game.
Really is a wonderful game though, thank you very much. A very enjoyable break from the normal hardcore gaming.
Have the Steam version by the way.