pupil said:
But for my purposes, I want square pixels as I will be playing this on my PC monitor. I've finished compressing the video, added the flag to make it 853x368 (56 pixels from the top and bottom of the image cropping the black bars as much as possible) in the mkv and it has come out at exactly the same resolution as the original DVD.
Wow, all this 4:3 anamorphic non-square pixels to 16x9 square pixels gets confusing. Glad you figured it out!
-G