I am using DVDA-3 and also have the screen go black for a second when the looping menu goes back to the loop point 'ONLY' when I import the menu audio stream as AC-3 (from Vegas). If I import the same audio stream as a wav file or as the audio track on menu avi I do not see the black screen when the menu loops. My video in to DVDA-3 is NTSC DV.
Your audio track and video track may not be the same length. Bring render into Vegas and check it. If true adjust, rerender, and loop should loop. John.