After 2 days I finally figured out why some of my mpg files were playying choppy.
Helpful software was gspot and directshow filter manager.
In gspot audio and and video would play fine individually, but when played together it would be choppy. The culprit was a codec installed by Hauppauge, aliasly called mainconcept. The codec was the HCW Layer II Audio Decoder which would kick in only when the audio and video played together. The solution was to lower the merit setting in directshow filter manager. Voila, instead of using the HCW codec, ffdshow kicks in and all is well with the world.