Almost all my video's are done with a gopro (hero2 and hero3 BE) and never experienced what you refer to. What settings are you using on the gopro, someone (even myself) can try the same to recreate. Otherwise I'd consider it's your video card not able to handle the resolution or frame rate - details of your computer would also help others assist.

Thanks for trying to help.. the video card is a Transcend micro sd hc1 class 10. I have shot videos at 720, 1080 and 144o at 48 and 60 fps without success

Have you tried playing the raw video directly through the TV? Or the computer? Same issues? Lower the frame rate, same issues?

Got the latest gopro firm ware?

I would Still be guessing its video card related, rather than software. Your other camera would most likely be at 30 frames per second which could account for the difference.

Example of my gopro footage below at 1440 res, 50fps (PAL). Pretty smooth.
https://www.youtube.com/watch?v=tLy-ycBz3nc&feature=youtube_gdata_player