Could be as simple as seat height. A good rule of thumb is...Knee pain in the front of the knee - lower your seat. Knee pain in the back of knee area - raise your seat. It couldn't hurt to try adjusting your seat first and testing this out. I used to have terrible pain on the outside of my left knee too - then I lowered my seat just a little bit - and it went away.
Best of luck to you.
"Things look different from the seat of a bike carrying a sleeping bag with a cold beer tucked inside." ~Jim Malusa
2009 Trek 520-Brooks B-17 Special in Antique Brown
2010 Surly Long Haul Trucker-Brooks B-17 Standard in Black
1983 Fuji Espree Single Speed-Brooks B17 British Racing Green