I suppose being super fit can involve putting your joints under some strain and wear. And you gotta work on flexibility and whatnot separately to most of the fitness stuff.
I'm 45 now and veteran of rather more physio (NHS and private) than I'd like to be thanks to various shoulder surgeries and mountain bike crashes etc. Enough that I can even ill-informedly speculate on why your knees got better! Had you done a lot of walking around that weekend as well? Apparently if the cartilage is thin and abused enough you can literally bruise the bones. And/or if you have bony ridges forming they can inflame the tendons and stuff, that's sore as hell too.
It's reasonably likely I have some arthritic times to look forward to sooner or later, apart from the shoulders I definitely have at least one foot heading that way (which is where I got that cartilage/bone bruising info from). Touch wood, my knees and hips seem ok so far, despite me being in A&E for a day last year when they thought I might have fractured my pelvis. That was another mtb crash, couldn't walk for a fortnight without crutches but nothing broken, woohoo! (the catalogue that day - no ability to put weight on one leg for the fortnight, plus a concussion and 40 minutes missing memory, don't think I was actually unconscious though, sore shoulder couldn't sleep on that side for a couple of weeks, and the thing that lasted longest was that I wrenched one of my thumbs and the ligaments were sore for weeks and weeks after.)
EDITED: 12 Feb 15:54 by MILKO