This could very well be where your problem is. The parameters in the screenshots in that tutorial are examples only. They are not a be all rule you should always use. Those were the parameters I needed to use for that particular video file in Sakura Wars. You need to look at your videos and understand the parameters of what your input video is, and what the output needs to be and make the appropriate changes.Then, I am literally your tutorial through VirtualDub and giving the parameters as in your tutorial.
I can take a look at those samples later, but can you also provide your converted MPEG version.