| Judging from your lack of an impact activity I am going to venture a guess that it's the sudden inclusion of a high impact exercise that is causing you this pain.
You should start running shorter distances at a slow pace on soft surfaces like grass or a rubberized track. that will lessen the impact on your knees.
As doug said there are many reasons that this could be occurring. do as he recomended...stretch and trying mixing walking and running.
as for your plateau...weight loss is easy at first when there is a lot to lose. its a lot harder during the last 10 lbs and diet plays a big big role in helping you get the last 10. | 
