I've had similar problems with certain video editing software and found a few things that might contribute - odds are something's running in the background that you don't know about or that you have space issues or free space fragmentation issues on your drive.
If you haven't done so, get "Ad Aware" and "Spybot - Search & Destroy" and remove all of the adware & spyware from your system (note that this may disable some programs which include adware/spyware).
If you're connected to a network and/or the Internet, disconnect from both so that there won't be any network traffic in the background.
Be sure you're recording to a hard drive with a lot of free space. If you're running Windows, it doesn't always (well never really) do a great job of defragging your drives. You can have no file fragmentation at all but still have a ton of fragmentation in your free space. This particularly becomes an issue when you're recording raw data that takes up a ton of space on a drive that also contains lots and lots of relatively small files - there's a chance that your large slabs of raw data are being spread across thousands of separate locations on your HDD. In theory this should present no problem at all, in reality I've seen it cause the sorts of dropouts you're experiencing. Matter of fact, the best solution if you can swing it is to install a separate physical drive for recording/mixing and regularly back everything up to CD/DVD so you can keep your recording disc very clean.
If all of that fails and if you know approximately when the problem started, work backwards through everything you've installed since (and just before) you first noticed the probem and uninstall things until the problem goes away.