Probably just a PC lag issue. This is the biggest grip I have with the concept of using a PC as a home theater solution. Unlike purpose built home theater devices, whether they be a DVD player, cable box, or a HTPC made to be a HTPC, using a standard PC means that you are running Windows, and using whatever hard drives were laying around at the time. You likely have anti-virus software checking everything, and some program or another is running out to the Internet every few minutes to check for a firmware update.
There is never an obvious answer as to why you are running into hiccups, but the entire solution of using a PC instead of a home theater product means that you are flat out accepting the compromise of pure quality. This obvious isn't an answer, but it is. If you want no skipping, then reassign the laptop entirely for home theater use, or go to a product which is designed ground up to do what you want. WDTV Live, for example, should not have any of those issues. Other NMTs (Networked Media Tanks) should also do a pretty good job at handling the A/V side of your collection without issues.
But, with just a laptop, you aren't likely to get perfect results unless you get rid of all the extra headaches that come with it... and make it a pretty good multi-purpose tool. Yet, as is the case, the dedicated tool performs much better than the multi-purpose tool.
