Mountain bike knee pain

Over the last few weeks I have been struggling with knee pain in my left leg associated with mountain biking. When I first started riding mountain bikes like any other newbie mountain bike rider, flat pedals was the way to go. As I got deeper into riding and pushed myself much harder I made the transition to clipped/cleats.
When I first started using cleats getting them set up for me was a pain in the butt. But however, when the set up job was complete my riding seamed to improve 100%.
I never suffered with knee pain for a least 2 years of using cleats. So when the pain struck, I was completely taken aback by it and I could not fathom out how and what would sort it!