Hi noticed this bug while testing annex, but when you remove the use of custom intro, meaning no intro at all, menu music starts playing up to a minute after menu opens. This only happens if you let "based on glest" transition to menu on its own. However, if you click to skip to menu the music starts immediately.
Currently using windows 7 64 bit
8 gigs ram
Nvidia card
However noticed this on my Mac Book Pro
and tomreyn noticed this on Linux as well