This started happening with the new build of stencyl, its cutting a tiny piece of the .ogg track which is making the loop not flow properly. I've got old builds of my games and the loop is perfect but if I open them games in the new stencyl and make a new build, the loop has been cut making a sort of pause then loop again.
if you have an old build of a game check it out, make a build in the new stencyl and see if it loops properly..
its obviously something on stencyls side, im sure they will fix it but it has become a bit annoying, don't know about flash i build in windows