Hi,
Using the latest release (1.0.0 build 1795, 64 bit) there is a problem with the pixel positions exported to the bundler *.out file format. This error occurs after aligning photos and then removing points using gradual selection with the image count filter.
A workaround is that after saving the *.aps file and restarting the program, the correct pixel locations are then exported by PhotoScan to the *.out file format.
-Jeff