Converting .vob to .mkv - result video is choppy

I tried converting .vob to .mkv or even to .mp4 and the result video is choppy. During motion scenes there is movement for a second then stops, then movement. I then took the same video and converted the .vob to .mp4 using Microsoft Movie Maker and it was not choppy at all, looked fine. Why would this be? I have a very fast modern computer with Core I7-3770k cpu, so it shouldn't be my hardware. Thanks.