First, let me say that this is a phenominal program. I just paid the $40 after trying the trial version for a couple of days. It is worth every cent.
I have noticed that when using 3d mode, the elevation data seems to be 100-200 meters west of the maps and gps tracks I have uploaded. I am working mainly around the Albuquerque NM area. BTW - the imagery and topo maps are dead-on perfect for this area when I upload GPS data. I took a GPS reading next to a big tree that was easily found on the aerial photography, and the waypoint matched exactly with the GPS reading about a 5 m error.
Brian