+1 on the repetitive nature of trainers. They fix you to basically a very narrow range of variable movements so, for example, you don't get the out of saddle experience (unless you have the Rock N Roll), you don't have the natural movement on the saddle for various situations (potholes, bumps, etc). On the road I suspect that a rider will make subconscious minute adjustments to accommodate minor twinges etc.
Although this is basically a wild guess it sounds like your saddle may be low. Knee pain under knee cap to me means the knee cap is always pushing into the leg. Knee pain behind the knee usually means the tendons are being pulled, i.e. saddle too high. I find that for myself I need the saddle a bit higher than perhaps some fitters might recommend. However my knees tell me that it's a good height.
Finally you may want to play around with cadence. 80 rpm is fine but try mixing it up. 100 rpm, even 110 rpm. By increasing rpm you reduce the peak forces on your knee, sort of like lifting 80 lbs 3 times or 60 lbs 4 times or 40 pounds 6 times. If in my super simple example 80 lbs at a time is too stressful it may be that you can get away with 60 lbs or 40 lbs, if you will.
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"...during the Lance years, being fit became the No. 1 thing. Totally the only thing. It’s a big part of what we do, but fitness is not the only thing. There’s skills, there’s tactics … there’s all kinds of stuff..." Tim Johnson