I would consider dropping the machine based work from your program (leg press and extension) at least until you get the pain under control. With those movements your are locked into a plane of movement that may not be ideal for your individual anthropometry.
You should also post some video form checks to make sure your barbell lifts arn't causing the issue.
Could you clarify where on your knee it hurts and how the pain progresses before, during, and after exercise. Some information on age, weight and injury history would also be helpful here.