Been having this problem for a while now, but I feel as if it wasn't always an issue.
Rendering any type of sequence as a multiplexed Mpeg-DVD file (.mpg) results in random choppiness when the video is played back in a media player (tested on WMP12, the latest Media Player Classic, and Windows Media Center). The choppiness does not happen when the file is rendered as non-multiplexed and then multiplexed in a different program such as TMPGEnc. Choppiness from the multiplexed .mpg is not noticable when re-imported into Premiere and previewed.
Premiere Pro CS5.5.2
Community Codec Pack
K-Lite Codec Pack
Uninstalling the codec packs does not solve the issue.