Dave I threw down a bunch of thoughts too. And I was impressed with the judge credentials on those sheets as well. Couple of Nationals and a Master. I don’t know if too cold will stress an ale yeast, certainly the altbier yeast and US05 can take 60F just fine. I’ve had British ale yeasts go pretty slow down that low though. I’ve never identified a problem but wasn’t looking either.
You seem to be doing everything right, so its a little perplexing. Its liable to be something small, but this kind of issue is annoyingly tough to diagnose and fix. I usually start from scratch and change a number of things rather than try to dissect and change one thing at a time. Maybe get a new autosiphon, a new bucket or two and/or a long soak in strong PBW, and hit your bottles and bottling bucket hard with PBW. That’d rule out infection. Then doublecheck thermometers and go from there. Since you mostly keg and enjoy your beer, it seems possible that its an issue associated with bottling.