Hi,
I have the exact same problem, VLC and Windows versions.
Since you suggested selecting waveout, I tried changing my output to Direct X (just to try something other than what it was already set to) and restarted, and that stopped the hiccups/skipping. Switching it back to waveOut, which is what it was set to originally, gave me back the audio hiccups.
So I tried the download version you linked to, and it did not skip at all when I played a file... and was set to waveOut by default. However, it is very touchy in that when I even minimize or maximize a window from another program it skips audio.
My computer is also decent - 6 core i7 with 12 Gigs of RAM so not sure whats up with that - v2.0.5 and all previous versions I've used never had such issues. (except the hiccups ever 6 or so seconds lately)
I guess I'll go back to 2.0.5 and switch to DirectX ... but do you (or anyone) have any other suggestions?
Thanks!
edit: PS - the vlc-cache-gen.exe came up detected as a virus by comodo when I was installing from the link you gave.. not sure what's up with that, just thought I'd mention it.