So, I recently switched to road from mountain a little less than a month ago. I would switch my seat hieght on MB according to the train. With the purchase of my Felt F5C, (excluding all the blown tubes) I have been really pushing myself on the bike and running. I have noticed a good increase in the 3+ weeks of riding. ~15 mph in the anerobic zone to ~18 mph at the border line aerobic zone. However, I have recently noticed that my knees are aching following the ride, and today during my 30 mile daily, I noticed a pain in the tendons connecting the hammy to the inner knee. When I bought the back, I had a professional adjustment, and I have stayed in the spinning state since I bought the bike.
Last year I was having problems with my knees as well. Mine came at about mile 90 on my long rides, hurt like hell and for a couple of days later. I always heard that turning a high cadence was the way to go, but when I slowed down my cadence, the knee pain went away. The pain came when i was operating at about 100 rpm's, it went away when I slowed it down to about 91 rpm's. Just my experience, don't know if it applies to you or not. Good luck.
i bet your mountain bike has longer cranks. It's common for MTBs to have longer cranks, which I reckon is kinda stooopid.
Longer cranks put more stress on the kness through the top of the stroke, due to increased flexion.
don't count out that you could be overtraining...tendonitis in the knees...when you rub ur knees, do they feel like they're tight, almost making a feeling like ur rubbing a balloon or something? i've got it right now cause stooopid me pushed my training from around 180 miles a week to 230-240 miles a week...shoulda eased up to it, but nooooo...i'm 22 and my testosterone wouldn't allow it...