I was having na issue when I play mp4 file shortly after the video starts a second of silence is inserted and throws out sync. This was especially a disaster because I was using directshowsource with avisynth and hardcoding the out of sync audio! I thought my source files were bad, but I have found a solution. Hope this might help anyone else with this issue.

I figured why not try reinstalling CCCP, and reregister all filters. When I ran it it did warn me Gabest splitter is on there and has been known to cause problems, so I disabled it when prompted. I replayed a video file I thought was a bad source, and now the audio play fine all the way through, and my directshowsource() woes have ended.