Video Got Crazy

I have a video (actually 3) that I recorded yesterday. I tried to use custom cuts to take out the commercials, but when I started to do the video, either the video is a little choppy or it studders. To make things a little worst, I’ve been having a little trouble with my computer to start with. But that’s on me I guess. Anyway, getting back to the choppy or studders, I ran the video through handbrake with no problems. After that, I ran it through MCEBuddy to take out the commercials. The choppy and studders came out during playback on the TV. So what would cause the choppy or studders?