First of all, congratulations for such an amazing and efficient software!! It makes high quality photogrammetrical reconstruction available for a large range of purposes. I am currently testing its potential in use-wear study of archaeological tools.
I recently wanted to compare the difference of alignment with and without pair selection (Generic/Disable) in high Accuracy mode and I got strange heterogeneous results from Photoscan Standard Edition 0.9.0 1584 installed in a TOSHIBA QOSMIO X500 (Intel Core i7 720QM, 8.0GB, NVIDIA GeForce GTS 360M). In fact, it seems that starting a new session (File/New) is not sufficient for clearing the memory since the subsequent Alignments and Geometries are then aleatory. Only by closing Photoscan (File/Exit) after each work, I can constantly get reliable reconstructions.
With the same sets of images and the same parameters but with version 0.9.0 1542 installed in an Asus P31S (Intel Core i3 2350M, 8.0GB, NVIDIA GeForce 610M) it is not necessary to close the software for successfully starting a new session. I don’t know whether the bug is due to the hardware or to the last release of Photoscan? I spent half a day before understanding that my set of photo-macrographs was not faulty, despite a low depth of field at 1.5:1 magnification (worn tip of a Palaeolithic quartzite tool), but that something else was wrong.
I hope this may help not going too fast in conclusion when making comparisons ...