I had an odd thing happen on my first alignment w/ 1.8.1 -
All but 54 (of ~2000) cameras aligned, and the unaligned cameras were part of a double pass on a shoreline with good features, good GPS positions (PPP with camera arms input), and no distinguishable difference from their neighbors, right in the middle of a gently curving shoreline.
Since I kept the keypoints, I was able to select only the unaligned images and "align selected" and they aligned perfectly with the others in just a few minutes, but the apparently random dropout makes it hard for me to trust an alignment workflow in any automated fashion.
Align settings were (from dropdown, not batch) - Accuracy High, Generic Preselection, Reference Preselection/Source, 60,000 keypoints, 0 tie points exclude stationary tie points checked, guided image matching off, Adaptive fitting off.
I attached the logfile (zipped because size) for the alignment in case it's useful.
Camera is Nikon D810, images are JPGs derived from RAW with Adobe Camera RAW at full quality, no chroma subsampling, Adobe Camera Standard color profile and no other tweaks. I have not seen this issue in 1.6.9 or 1.7.5 (didn't play with other intermediate versions).
/andy