Choppy Video at Specific points

I finally got my minidisk video onto my computer through a connected dvd-rom drive and then converting it to mpeg with handbrake. Once the video was in iMovie i set about splitting the chunk into chapters and taking out bits that I didn't need.
However, in places where I took a bit out or where I added a title the next clip skips and is incredibly choppy. The music works fine, though. I thought it might be the computer at the time but I have saved/reopened/restarted and nothing seems to work. I even exported the project to iDVD but it is choppy there as well.
I'm afraid to burn it to DVD because I only have a few at the moment and I'm not sure if it'll work itself out. Any thoughts?
Thanks,
Alex

I can't address the chopiness itself.
But if you want to test whether a DVD would have this same problem, you could save as a disk image. After it renders (this can take many hours, mind you) you can view it in the Mac DVD Player. That will show you exactly what your DVD would look like if you chose to burn it.

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