Hi again Marcus and Stephan,
Yes, correct - the HeapSort was specifically the problem.
As I was not too specific before :-), here is the main bit:
"HeapSortAlgorithm.java 1.0 95/06/23 Jason Harrison
Copyright (c) 1995 University of British Columbia"
Would omitting only this file disable TLC or anything vital? It seemed that this is perhaps part of a layout algorithm for translating to TeX, so I assumed that would be a "nice to have" vs. part of the core functionality.