I agree that the ballots were most likely .pdf files and were read by Adobe Acrobat just so they couldn't be edited.
But you can still dink around with the printer settings like fit to page, print full size, etc.
However, a 19" ballot vs. a 20" ballot shouldn't have mattered to the scanners, and here's why:
The ballot is printed with guide bars along the top and left sides so that the scanner can calibrate itself to where the bubbles are. The scanner should have been able to lock onto the guide bars and read a 19" ballot just as easily as a 20" ballot.
Something was set in the scanners that prevented this from happening. I don't know if it was accidental or intentional, but it shouldn't have made any difference to the scanner whether the ballot was printed 19" long or 20" long as long as all of the guide bars were intact.
Here's an example of what I'm talking about:
