what I did is I started warming up on the bike doing a bike build, increasing resistance(to a good hard working load) and breaking a good sweat. That seemed to have gotten rid of my knee cap pain when squatting and I wasn't even squatting heavy either.
it's my surgically repaired kneecap.
dec 2006 I sublaxed L patella while running my 1,000th lap of Bolsa chica wetlands when I lived there and ran a lot...to keep ip with mark and the boys on our saturday morning main divide via silverado/maple decent runs. didn't you join us on at least one? usually 3-4hrs.
happened on the levee. stepped in a hole on the side of the levee, running at night. random! ripped off the articular cartilage.
surgery removed the floater, and It's been fine since. I still feel
it walking up stairs or squatting. after a long warmup like you described it's less of an issue. stretching quad and hammy helps as well to allow proper tracking of patella.
I joined you guys on one run that blew up my calves on the climbs.
I think I remember! They always started hot running up silverado.