Can you move to the center of that map and save it as a new name.
Press G and F to switch from ground mode to free flight
Re set the start marker. I saw a map like this where there was a start marker under the terrain at this spot.
Save, and then reload that map.
Give that a try.
Now what happens if you make a new flat terrain map, and place 1 building and 1 start marker and then save while your in the middle of the map? When you call up that map does it stay at the position you left it?
Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz, 2400 Mhz, 4 Core(s), 4 Logical Processor(s), 8gb RAM, Nvidia gtx660, Windows 7 Pro 64bit