I've found this is browser related. Here's a small experiment.OnEndLooping.capx
IE has a subtle delay (less noticeable in this example, but if you switch to looping the same track, you can here it).
Chrome has no delay. Firefox has a terribly noticeable delay.
Also maybe double check that there is no small delay at the end of your intro music file. There was a thread about a small pause being added by the C2 converter, under certain circumstances.