Hi Peter -

I can't really see the image you posted, but I seem to understand that you are not getting enough warping, rather than too much, correct?

In that case, I have a few general comments:

1. If the area that are not properly aligned are somewhat large and/or somewhat far from each other after registration, you may want to make the initial control point spacing coarser and also make the optimizer take larger steps (not sure how that translates to arguments for the munger script that I assume you are using).

2. If the misregistered areas and/or the residual displacement are somewhat small, then relaxing the constraints of the warping by reducing the penalty term parameters (again, no idea what that means for munger) may help.

Basically, the idea here is that misregistration could result from either things being too far apart in the initial configuration (which could be improved by 1. above), or from the warping being to "stiff" to account for the true complexity of the difference between your images (which would be improved by 2. above). Obviously, the distinction is a bit fuzzy (what is "somewhat" exactly, right?), and it may well be that you have a little bit of both problems.

Hope this helps a little, and perhaps Greg can fill in the munger gaps in my knowledge.

Best,
  Torsten