The other stuff is under AA control, but being selected to use pre-check is NOT. When you looked at your profile for that flight, did it show pre-check under your GE number?
Well, I think it did at one point but I didn't check more recently. But neither of us got it, I've never been denied in the past, and not a single person went through while we were waiting in the regular (elite) line. So I really don't know for sure what the deal was, and I gather we'll never find out. We'll see what happens on the return.