Cpu load of the game is too high.
Quality settings of Fraps need to be lowered.
You probably already checked this but make sure your code is running efficiently. Running Eclipse + your code + Fraps might be reaching a bottleneck that a game + Fraps doesn't.
Are you isng LibGDX or something else for your base code?
On a related note: I recommend checking out VisualVM, it's free software that monitors any JVM running and will report to you useful statistics such as CPU usage and time spent calling each method.
Pre-Post: 65K beat me to it lol
I have a hard time believing that my barely 500-line code - even if it is potentially unoptimized - can cause more problems for Fraps than mainstream AAA games on high settings...
All I have is a ball that can be controlled to move left, right and jump + a few platforms
Box2D's DebugRenderer is running though... haven't thought of turning that off yet before recording...
Yup, I'm developing using libgdx