Thank you for your reply, and I am sorry for the delay on my part. We looked at the commands used for the affine registration, and found that adding the "--auto-multi-levels 4" option seems to have helped increase the success rate.

So far, we haven't experimented with the idea of using a preloaded affine registration, but it sounds useful as a way also of reducing computation time, since most of our images are consistent in size. Does it just mean that we would re-use a registration from one of the successful jobs (perhaps after scaling/rotating/cropping the image in advance to ensure some level of consistency)?