I believe I've solved the problem. I've copied in boxes made from queXML and placed them over top of Calli's boxes (which have no dotted lines). Doing so made it all work. As for the verify page, Adam correct me if I'm wrong, it appears that it doesn't resize the actual image, but does take into account resizing when scanning in the answers. We can assume a human user would be able to figure out that each box might be a little off. Ideally the image would be resized to assist the verifyer but it's not a big deal IMO.
As for the boxes - the administration manual states
3. Boxes to be filled in should be square or rectangular (not circular)
Calli's boxes seem to fulfill the requirement but do not work when there is any skewing or resizing, as there always will be with a scanned image. It seems this must be a documentation bug. I am unsure specifically what it is about the boxes that is required. I would guess the horizontal line is actually a requirement. Perhaps the size and box line width effect it too. Here is the file I used. It's obvious where I inserted some boxes so that you can see the difference between them.
If the documentation can be edited wiki style I would be happy to contribute any observations I make.
A unrelated issue in page setup it says "Scan the form to a PDF using the same options that you will for the filled forms"
Doing this would result in the interactive banding being off. This would make it very difficult to use interactive banding. Wouldn't it make more sense to set the page width and height to the original PDF. Then verify the scanned sheet? In my case I used the original PDF width and height, but then modified the boxes that locate the corner lines so that it would work with both original and scanned files.
When I go into verify a page, the alignment is off. I've uploaded the
original pdf and the filled-in, scanned image into page setup and made sure
my config values were set so that the lines were detected on both. I
attached a screenshot of the verify page. You can see the guesses are off,
and it gets worse the further down the page. It appears that it is not
resizing the scanned image.
What would be causing this?