I had some issues while making movie clips in flightsim, and I thought FRAPS was the culprit.
The sim would "hook" momentarily, very irritating.
Turns out Java's prefetch was starting up and running in the background, and hogging the machine.
If like me, you are running Windows XP, you can disable JQS.exe:
http://java.com/en/download/help/quickstarter.xml