Time dilation - excellent. Must admit I haven’t thought of that… 
Benjy, it’s probably the right thing to do to get some stuff finished that works before continuing with the trouble child. Sometimes after giving it a break, things just resolve themselves.
I have another observation that puzzles me a tiny bit. For my latest projects, I usually don’t do the ratcheting any more since all I need is one alignment (K+ Brown 4 tangiental, MRE 2.0) with exif grouping followed by another one with no grouping and I get 0.3/0.4 Median and Mean Errors, which I think is quite acceptable. Tightening the MRE often introduces areas with no or insufficient Tie Point coverage. So I wonder if you could improve your errors elsewhere in the process, for example by playing with the distortion model. Your optics should be way superior to mine, so you should be getting better results with the same workflow. In theory at least…
Kevin, but shouldn’t starting an ENTIRELY new project and loading all images ANEW into it resolve any issues that might have been introduced as corruption along the way? I am certain that I have experienced similar issues of corruption and it has even been officially recommended to make backups before each and every step for exactly that reason (which in my view is almost unrealistic because it’s not worth it for small projects and can easily get out of control for large ones if you don’t have a huge infrastructure at your disposal).
I’ve read about the problem of the fixed index before but nobody has ever put it so clearly as you have just now. Thanks for that! In that respect it is all the more worrying that it is not possible to influence the order in which the images are being indexed short of dragging them in one by one…
It’s really quite a shame that there are no comments from the DEVs on this at all. Like you hinted, Kevin, it is almost impossible to prevent difficulties along the way of expanding a code like this. So I wish there was more openness on the side of RC because an enemy that you know is much better than one that is lurking in the dark. If we knew where the problem is or how it may be caused we could probably work around it and wouldn’t even feel the difference after a while. As it is, it is like Russian roulette…