There could be other programs causing the same issues even if you don't use RescueTime but are having the same problem. To troubleshoot do the following.
- Close out of the java program that is locking up.
System Preference > Security & Privacy > Privacy > Accessibility.
- Note with items are check and then uncheck them all.
- Restart your java program and attempt to reproduce the issue.
- If it is working correctly then quit, re-enable one item, and try again until you find the culprit.
- If you can't get around the error even with all Accessibility options off that you must have some other issue.
Anyway if you find any items fix the problem you can just leave them off though they might hinder there applications functionality.