And it's not cos I'm kneeling down too much.... ;-)
After running on a treadmill (only for a minuet or two at a time cos I'm new to running), I find for the next few days my knees really ache. I've got new trainers (MBTs), try to have a good technique (ball of foot down first rather than heel) and have used knee supports - neoprene thingys.
Bummer.
You can't get more gradual that a minute at a time though can you? One minut run, two minutes walk - that's what I'm doing. Pathetic - I shouldn't be getting pain after that surely?