Steve Bailey is the resident GE expert, he will probably post on this topic when he reads it.
A couple of things to keep in mind though, unequal, means the plc logic is not equal to the logic in the laptop your downloading from. Have you made any changes to the plc logic while you were online with it, but not in run mode? changed a contact? forced an output? etc. That's usually what happens to me when I get an unequal error.