I found a sequence that would lock the application because the "deletePlotElement" would hit a runtime exception. This was because of the units of a bundle where not all the same (m,m,km). (m,m,km shouldn't be a problem but looks like it's not supported either, a bug for another day.) Here's the procedure:
1. plot http://sarahandjeremy.net/~jbf/autoplot/script/demos/jeremy/mytracks.jyds
2. [menubar]->File->Reset
I put in a try/finally where the lock was made but not released (in deletePlotElement) because of the runtime error. I put in code to fix the runtime error in SeriesRenderer.
I need to go through and make sure all locks in a try/finally block.
I must have done this at some time, I've verified proper use. Closing the ticket. Java 8 has its own Lock object which should be used, but that's a different issue.