The Perl code had a bug, but I found it!

The bells-and-whistles version of the Perl model of USS evolution still had a bug, which became apparent once I fiddled the fragment scoring system to strongly favour good matches, and turned off mutation of the genome sequence (so only the fragments mutated). The bug manifested itself in the program cycles stopping, at fairly random points in the run (never stopping twice at the same cycle number or genome score, as far as I could tell).

After a LOT of careful detective work on my part, entirely unencumbered by knowledge of any Perl debugging tools, I found that a 'while' counter was being incremented at the wrong place (inside an 'if' instruction that was inside its 'while' loop, instead of just inside its 'while' loop). I still don't understand why this would cause the runs to stick at random points, but maybe the undergrad can explain it to me tomorrow.

(Confession added later: Solving the problem was not just the result of my careful detective work. The final discovery was helped by luck. I had added an 'else' statement to print a report that the next step had happened, but had incorrectly inserted one too many } brackets. In solving this I accidentally removed a different bracket than the one I had incorrectly inserted, which moved the while counter outside of the 'if' loop and, I discovered, eliminated the stopping problem.)