While waiting on my client...
I've been following this thread for the various ideas. I know you're very particular about caring for your animals, however, this reminds me of a long yearling colt we treated in Texas.
His symptoms had been presenting for at least 10 days. Washing, sheath cleaning, pest treatments and an extra deworming had been done with no imorovement. Bedding had been stripped (he was in the show barn) and he was on dusk to dawn turn-out. During day stalled and under fans.
Finally had to have vet out when he'd rubbed tail down so that it looked like it had been banged (trimmed) to an inch beyond end of tailbone. Vet started her close-up inspection of the anal area and tailbone. She was expecting to find a small sliver or slivers that had abscessed, causing irritation and rubbing. What she found was a BEE STINGER with the pouch still attached just before the tip of his tail!! It was on the outside edge, buried in all the hair. We all found out how sensitive it was when she touched it with the forceps. A kick is putting it mildly...ended up having to give a mild sedative so that she could pull the stinger and scrub it down.
We used an antibiotic cream for about a week, but once that stinger was out, he got back to normal by the next day.
I'm not sure what kind of stinging and biting critters you have in your area. And if your weather has been as inconsistent as ours this year (winter for 2-3 days, then summer, then winter, then fall, back to winter) it's possible some non-seasonal bug got him.
Or if he's intact or super-sensitive to touch, the pleasure he gets from rubbing may outweigh the pain. Not saying he's a perv or anything....*shrug and sheepish grin* ....