I am working on relatively small (100-300 lines) Javascript files in Eclipse and periodically it gets really upset about some piece of code and pops up this error every time
An even better answer (from the bug report linked by Cliff Ribaudo, comment #10 and others):
Turn off Toggle Mark Occurrences (Alt-Shift-O or the paintbrush icon on the toolbar, which handily, will show you your current state).
Thanks Cliff!
Edited: