Since this is a question of a painful situation, let's be precise here:
The rule goes: pain in the front of the knee means saddle is possibly too low. Pain in the back of the knee means the saddle is possibly too high.
You talk about pain behind the knee-cap, which I would understand as still in front of the knee, i.e. under the knee-cap, which is a common site for cycling-related knee pain. (I raise the point only because Oxologic seems to understand it as behind the knee). I have experienced pain "behind the knee", i.e. on the back side of the leg. Lowering my saddle did help.
But, you should also assess the front-back position of the saddle, as well as, your gearing and cadence. Pushing a high gear at a low cadence (below 60 rpms) is a common source of "front of knee" problems. This is often reported as pain "under the knee-cap".
As stated above, if it *really* hurts, see a doctor.
Best of luck,
Jamie