The 990 is measuring the delay from when it puts out its test tone until the microphone detects the sound. So you have not only the time delay associated with the distance from the speaker to the mic but also any delay in the driver, the cross over, the wiring (negligible) and your amp.

My guess is that the system is detecting the extra delay caused by your electronics and compensating that out also. Two feet is about 1.8mS of delay. Finding specs on amplifier and cross over delays is difficult though so I don't know if this is reasonable or not.