Alexey,
So is it possible to get camera positions from first set of images using Tools->Export->ExportCameras and grab the X Y and Z from each camera . For example I'd use X=3.9532771096777926e+000, Y= 8.4841076306859320e-001 and Z=8.3161099324315579e-001 for camera 10...
<camera id="10" label="15223208-2015-11-03-160146.jpg" sensor_id="0" enabled="true">
<transform>8.7604856958468902e-001 3.1752547827018696e-001 -3.6292764344688505e-001 3.9532771096777926e+000 -3.6494470045003591e-001 9.2850052972977926e-001 -6.8572092756111175e-002 8.4841076306859320e-001 3.1520512264564143e-001 1.9252100389518070e-001 9.2929080148096688e-001 8.3161099324315579e-001 0.0000000000000000e+000 0.0000000000000000e+000 0.0000000000000000e+000 1.0000000000000000e+000</transform>
</camera>
I then create a .txt file with image file name and the X, Y, Z position in the method above. I load in my contrast enhanced images, import the txt file in the ground control pane then run Align Photos. The X,Y,Z positions measured by PhotoScan during image alignemnt are nothing like those I imported in ground control pane.
Am I misunderstanding how to use the GCPs as camera positions?