My son's knees started hurting at about the same time (3.5 yrs). Mine did as well when I was young. I remember waking in the night crying in pain...it seems common, so I'm doubting arthritis for my son (no swelling, redness, just pain when he's finally resting). When I would wake, my dad would rub D.M.S.O. on my legs and the pain would vanish. It's actually a muscle relaxant for race horses that you can usually only get from a vet (and some animal supply stores). I hadn't been able to find it for my son, so I bought some of my mother-in-law's mint cream (which has essential oil of spearmint and peppermint in it) and rub that on him. It at least gets him through the night and helps him sleep. Sometimes I do a combo of motrin and the mint cream, if he's having a really hard time getting rest, but that is rare.

Another theory (my own) is that 3.5 is when kids start really PLAYING I mean: jumping, running, rough housing with siblings, etc. and so the joints get jostled a bit more, and are getting stronger, as I out grew it, and his pains are coming less and less frequently (he's 4 now).