This isn't terribly surprising. RTA's and level meters have a lot of trouble with bass frequencies. It requires a lot more processing for those devices to accurately gauge bass performance. For instance if you look at the Galaxy Audio meters , you will notice that the CM130 is half the price of the CM140. But the CM130 is only rated down to 125hz, where as the 140 is rated down to 31.5hz.

Also the human ear can easily be fooled while listening to pink noise going from speaker to speaker, and suddenly to the sub. So a sweep works better since you are continuously listening as the tone changes pitch.

Now since I don't own a 990, and am not familiar with its programming, I can't state whether or not Outlaw dedicated a bunch of processing to that feature to ensure truly accurate bass setup. But it is possible they did, and in that case mic placement and sub placement issues could have caused the mis-alignment in your system. Moving the mic or sub just a small amount (a foot or so) could cause it to end up in a peak or cancellation node within your room.