Misplaced frames after conversion
 

so, I finally got me a device to record my gameplay, so I can record VG CGI scenes in HD. All's good. The raw files play on my PS3 flawlessly. Only problem is, there's a bit of gameplay (few seconds) before and after each scene, which I've been trying to remove.
With Pinnacle Studio 12 I can cut the file to just the section i need but there's no option to only do that, it makes me convert the file as well to "make movie".
After i do this and go to view the finished video, the quality is the same but there are misplaced frames every so often throughout. Anyone know/understand why this is happening?