Perhaps a video, or a sample scene would help explain the problem.
Are you using any of the retiming features in Krakatoa to change the playback speed? The playback graph can be used to make files play back “slower” than 1 frame of PRT per frame of rendering, but this can make bizarre motion artifacts when it switched between the “nearest” file to load from.
If you aren’t doing that and are just loading a sequence of PRT files without doing anything fancy then I’m as confused as you are. If you have your PRT Loader in the viewport and scrub the timeslider (use the time configuration dialog to turn off “realtime” so that it doesn’t skip frames) does it jerk like that? Does it have stuttery playback if you make a new camera that isn’t animated?
If non of the things I mentioned turn up any clues you should submit a few of your PRT files to us via a support ticket (support AT thinkboxsoftware DOT com). Preferably any two frames that are adjacent to the jerkiness as well as the scene with the camera, lights & PRT Loader. I’ll take a look into it for you.