OK, nevermind. I have come to the conclusion that this is not possible with mkv. If I change to mp4, then crop shows up and works. But mp4 is broken and not usable for DVD ripping.
I need to crop a video to eliminate some of the letterboxing. Autocrop does not do the job correctly. In the user manual it shows a video edit dialog that contains Crop/Effect/Watermark/Subtitles/Audio/Speed. I only have 2 options Subtitles and Speed. How do I get the editing functionality that is missing?