saddle angle and knee pain

After many hours of riding it appears my Fizik saddle angle was set all wrong (nose too tipped up). After finding Fizik a youtube video I set the saddle angle correctly. I now find it a lot easier to be more aero both on the trainer and out, and generally can position myself a more forward in the saddle.

But.... after few rides on the trainer, I started to get pain in the front other side of my right knee. At the same time, my training intensity has increased/changed to a lot of climbing and low cadence work.

My question is. Can change in saddle angle (even to a correct one) can cause knee pain? was thinking to maybe move my cleat backwards a mm, but wanted an opinion before I start to tinker.

Thanks.