Took me ages to find the solution to this.
Zend Studio would randomly stop working in the middle of something, whenever you tried to open a new file or change folders it would display this error.
Trying to restart Zend wouldn’t work either, Java would crash.
It happens when you are running synergy at the same time as Zend and you copy some text between computers. Not sure why it kills Java, but it does.
Easiest fix is to restart synergy, in my case it’s just:
# killall synergys