The one time (out of 9 trips) I got the big "X", I was also escorted to a special room (JFK, T8); but was out in about 5 minutes--the agent guessed it had something to do with fingerprints. [Instead of being cleared by the first available agent.] I was not subjected to any customs agent searches.
I did receive an email from GE asking me to describe my incident--you may also get an email. I never got to the point where I had to verify (on the GE terminal) the flight on which I arrived, it spit out the slip with the "X" early in the verification process; how far did you get when the "X" slip appeared?
PS: When I went for my GE interview, the agent noted that "X" can occur for "unexplained" reasons, and that I should always have a customs slip filled out just in case.
I got an X one time going into IAD from SIN/NRT and went to the first booth, and the agent looked at it and asked if I was carrying any fruits or veggies I said no, he said "ok the machine came up that way....a glitch"...he stamped it and off I went.