Hi Trevor.
Here's a couple of links I found:
http://www.albinoblacksheep.com/download/animationshop
http://www.pcworld.com/downloads/fil...scription.html
It does let you move each frame to register them against each other properly.
I use photoshop for that first - I copy each image as a new layer onto a new image. I then blink on and off each layer and use the move tool to align each layer with respect to the one beneath it.
I then use the "export layers to files" function in photoshop to save the layers as TIFF files. I then open the TIF's in Animation Shop to produce the animation.
Hope that helps.