God damn if I didn't run into the strangest shroedingbug just now.
After an hour of confusion, I restarted NetBeans to find that everything worked again.
Phew! In the course of tearing my hair out, I placed some choice (n00b) debug statements
and slightly altered the test file. Also modified the options slightly.
Did a bunch of finangling and ironed out some segmentation bugs on the way.
With some tinkering I found a segmentation scheme that gives slightly better results
than the current pipeline, but it's still on the road - not quite there yet.
A big note is that the test class either needs to be rewritten for this heuristic
or the heuristic for the test class. Test-driven vs. event-driven development...