I scanned a map in JPG format and calibrated it but it didn't work ie the calculated center map coordinates were always wrong.
I translated the map in GIF and calibrated it the same way and it worked perfectly !
I think there are some trouble with JPG.
However FlightTrack is a wonderful soft :-)
There is an issue with the calibration of maps when the resolution is not the standard 72 dpi. This happens when you scan a map, which is not uually performed at 72 dpi.
One possibility is to open the map with something like GraphicConverter, and change the resolution to 72 dpi. The map should not be resampled to preserve the quality.