I'm sorry, I missed the fact that this was on Athena. I've tried to look into the bug a bit more, but most of the reports on it seem to say that it stems from a bad installation or config file. Is there anything strange about your configuration?
You're probably right, that there was a problem with some eclipse config file. For future reference, we were able to fix the problem by deleting all of the eclipse-related files/directories like ".eclipse" and ".lasteclipse31" from the student's home folder on athena.