There apparently are multiple reasons for getting an 'X'. The one that does not seem to be publicized is that if you've been arrested in the past, you will get the 'X' the first time. While there are many accounts of people having trouble getting GE because of past arrests (even when later dismissed etc), this 'X' is showing up, obviously, after you have been approved.

It is quite odd, since the application only asks about convictions. At the interview they ask you if you've been arrested. If you have been they do not approve you on the spot there is some additional review, which can take a week or two. Then once you are approved you get an 'X' the first time through GE, where you'll have to go through additional screening (which you would never go through in the regular line). After that you have to call your GE office to ask them to suppress 'X'. Which may or may not happen.