Applying a freeze-effect to a cropped clip doesn't seem to work in 0.9. When 'Freeze Before' is checked, it does not freeze at all, when 'Freeze After' is checked, it does freeze, but 'Freeze at' counts from the beginning of the clip, not the crop start.

I can confirm, this is a problem in the MLT freeze filter. I just sent a patch to fix it in MLT.