Nobody can tell you anything. Sorry, but you're just throwing generic and vague statements. What does "messed up" even mean? You have to be a lot more specific and provide info on your project, effects used, render settings, system info and ultimately how you review your output. For all we know yolu could simply be attempting to play a hunky QT file from a slow drive and then the player skips frames...
UPDATE with more details: The videos that I'm making are simple, I'm mostly just adding keyframes. As far as rendering goes, I've tried multiple settings to see if it would fix the problem but nothing has worked. I generally use the best render settings and lossless for an output module, although I have tried the various QuickTime output options. My videos aren't too long either, they range from 5-30 seconds. When I open them in QT, some frames are missing. I also experience that my transitions which were key framed weren't nearly as smooth as they appeared in AE. My whole video is just choppy. I feel that the problem might be when I first load the movie on to QT and there is a "converting" screen. Maybe things are getting mixed up when QT converts my video. I would also like to add that this has not happened with any of my videos from Final Cut Pro or any other Programs. This has been happening ever since I got AE. Hopefully I have provided enough info, and again, help is very much appreciated.
Sorry for this issue. Did you ever find a solution? Please let us know if you have or if you still need help.