I think the major question here is, is every thing you export from WMM showing up with skiping audio, or only projects with the footage grabbed from this site? The next question, if it is only footage from this site, are you getting rid of the audio on those clips or are you using them in your projects?
Considering as you say, you take webcam footage and put audio to it then the project turns out fine. I can probably take a guess that it is indeed those clips you are downloading causing the problem.
However, my biggest question here is, what do you mean by skipping? Is the audio/video not synced? Or do you hear clicks and pops and other odd problems with the exported video?
Depending on your answers, the solutions could be different. Just from what I have read so far, I would say that your problem is that you are using badly compressed audio in your video and it is wrecking havoc on WMM's encoder. And if that is the case, the solution is, stop using badly compressed audio.