CS5 Photomerge - incorrect reposition/alignment

Hello,
Im an architecture student using educational version of CS5, and recently I've been having an issue(?) with the photomerge tool.
A little background to what Im trying to do: Im working on a project that involves taking screen-shots of a 6 square miles area from Google Earth and combining/tiling them to obtain a bigger, more detailed map. I have the Google Earth set so that it shows only the satelite view of the ground below, with all the ground effects turned off (simplified and flattened ground) and from the same altitude/zoom level.
When done, I had exactely 120 screen-shots, which I ran through photomerge set at reposition only option. At first, PS loaded all shots and started aligning them, but would take forever to complete. I tried tiling groups of 12 shots at a time then combining the results, and that worked great. No problems here.
I had to relocate my 6 sq mi area to a different place and redo it all over. This time photomerge would still work (still grouping shots), but it would not position them correctly; meaning they would be on the bottom instead on the top. I tried overlaping the shots more and ended up with a total of 144 files, but with same results. Most of the screen-shots would be positioned correctly, but sometimes photomerge would divide the map in two with a blank strip of nothing. Sometimes the map would be 98% correct, with shots positioned, aligned, and blended great, except for a last row of shots that would be detached from the rest of the map.
What am I doing wrong?
Any input would be greatly appreciated.
Thank you!

Thank you for your reply.
Well, all of the 144 screen-shots taken have the "Google Earth" and two other marks on them, but I made sure the shots overlap each other enough so that PS have room to work on them.
I made a couple attempts on the same set of shots (with marks on all of them) and most of the time photomerge tool won't have any problems with correctly alignining and blending them. There were a few instances where a row or a column, depending on how do I 'stich' the individual shots, would be correctly aligned within its row/column, but wont align with the rest of the shots.

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