To set the duration of a loop you must do it on an empty loop.
One other thing to note, all track lengths will be set while recording Track 1 (and 2 if stereo recording) on an empty loop. All tracks are always the same length. So if Track 1 is 6 beats, then Tracks 2-6 and Mixdown will also be 6 beats.
Thanks so much, that did the trick!