Yes, knee pain can be delayed on the bike but I would agree that this is not likely the issue.

If it's the lunges to the side that are the problem, you're having a problem in the frontal plan with stabilization or form. The major components of cycling motion do not occur in that plane of movement (at least they shouldn't), so they are unlikely to cause overuse injuries related to motion in the frontal plane.

This is a good overview of axes and planes of motion if you want clarification of what I mean by frontal plane motion.