This is realy redicurious thing I have heard about. Ask yourself what could cause this, don't answer me here. If you think CIS was wrong, then THINK a way out, like below. If you think you are a person most wanted/unwanted by FBI, then FIND a way out.
Write a letter to the director of CIS to explain your situation. If you have problem in security check, the I-485 application may get trouble, but not EAD.
Ask a senator to seek help/direction, like "what you should do to get EAD".
Write letters to the directors in different centers where your file could be.
Let see Xiaobotu's suggestions.