It is sunday and You working? What a job? I think You want to encode DVDs to KVCD, right?
Which version of Moviestacker do you use?
I think your source is a d2v created with DVD2AVI 1.76, if not get this version.
Next You load it in Moviestacker. In Version 2.00 beta 3 You can chose the resolution in the first page. If Your movie is 4:3 take anamorphic out and mark UseCripFit.
Full Size
Full Size
Try using the resolution 704x480. Thats the resolution I use with my DCD-Video-Template. I never had problems like You.
Normaly if u chose in Moviestacker the KVCD-profile the right filters will be added to your script.
Try out the MA-Script. Read my Guide for
CQMatic. There I described how to edit the MA-Script for Your case.