The scrambler that I wrote I got around it by not selecting a random face, but selecting a random axis, then choosing one of the faces on that axis, then a turn. I.e. Pick one of x, y or z, if you pick x, then pick R or L, if y, then U or D, z implies F|B, finally, pick the turn of 1, 2 or -1. All you have to do is ensure that you don't pick the same axis twice in a row and you eliminate the scenario benjediman describes.