Thanks everyone for your suggestions. We have it working now. For some reason, it appears that when we changed from capture and sequence presets of 23.98 to 24fps, it synced again. Unfortunately, we were changing multiple variables simultaneously, so we're not exactly sure that it was that simple. Understanding that the 24fps on the SDX900 is really 23.98, shouldn't we capture at 23.98? If not, how is FCP recording the video at 24fps, is it adding two frames for every 100? And is it stretching the audio?
Again, thanks everyone.