I know there's a couple of other non-geared knee pain threads, but mine seems to be different. I have a couple of knees that I abused during my younger skateboarding days and I've been riding singlespeed for 6 mos. now with no knee pain. Now that it's cold, though, I'm definitely getting pain under my kneecap in one leg. What seems different from everyone else with gimp knees, though, is it's only a problem for the first couple of minutes of riding, then all is as normal. However, going up and down stairs is now kind of painful - I have to sorta turn my foot to the side. Not awful, but annoying.
I've been riding a SS mountain bike with a too-small frame, although the seat height is fine. Gearing is 45/18 (on my non-snow bike, it's 47/16). I'm also using cages where normally I use clipless pedals. My stroke is not great - the bike definitely goes side to side when I'm standing - but again, never had a problem when it was above freezing.
There's an off chance that riding isn't related to this at all... but just for curiosity's sake, anyone else have similar experiences?