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
At first I thought this was just a trick, but it is working so well, I had to post it as an actual answer.
When the error window pops up, don't close it. Just drag it off to the side, focus back on the main window and keep editing.
When the error happens again Eclipse doesn't change the focus back to the error message. Focus stays in the editing window and you can continue to edit the document.