Leg length discrepancies will likely effect knees but so will pedaling at too slow a cadence. To slow pedaling is a common occurrence in new cyclists. This is equivalent to an internal combustion engine trying to take a hill in too high a gear. The engine will lug down and sound unhealthy. It does take some practice to get up to typical cadences for longer rides of, say, 85 to 95 RPM. This may not be your principal issue but it is something many of us newbies have to work on. I occasionally do a ride where the focus is to spin the pedals.