Cryptic Crossword: Amateur Crypto and Reverse Engineering

http://www.muppetlabs.com/~breadbox/txt/acre.html

Something that my friend had noticed was that when we scrambled a puzzle twice in a row, the two keys would be different, but only in the first half. The third and fourth digits were the same. At first I thought that this might be due to scrambling the same grid, but further exploration suggested that it was entirely due to temporal proximity. So naturally, I tried running two instances of the Across Lite program at the same time, and hit Alt-S S on both of them as quickly as possible. In this way I obtained two grids scrambled with the same key.

With this technique, I had my first inroad, a way to start making some actual progress in the investigation. I could now create two crossword grids that differed in some specific way, scramble them both with the same key, and then compare the results, seeing directly how a change input affected the scrambled output.