Have you ever jumped back into full-on training too quickly after some time off and experienced a nagging pain not in your knee itself, but in the joint behind your knee. It is one of those pains that you can run through, but man does it hurt. If you try to ignore it, it does not go away. It gets debilitatingly worse, as a matter of fact. What you are experiencing is gastrocnemius tendonitis.
Your gastrocnemius tendons run from the top of your calves through the back of the knee, as pictured above. When they get inflamed, there is a lot of negative friction that occurs in that area. Amp up your training too fast, before your body has had a chance to make the correct adjustments, and you are just asking for it.
In high school, especially after a vacation, I often times experienced this nasty sensation. The best defense against it is to make sure, no matter how good you feel, that you aren't putting in too many miles too soon after time off. Maybe your lungs feel okay, your heart can handle it, and your muscles aren't complaining, so you think running a few extra miles won't hurt. Think again. Always get back into a serious training routine in steps, and make sure the first step is gradually exposing your body to more and more mileage.
If you start to experience pain on the back side of your knee joint, you need to deal with it right away. Cut your mileage down, or skip some training days altogether to get a handle on it. Ice it religiously, ten minutes on, ten minutes off. Keep it elevated when you can. Also, use over-the-counter pain and inflammation meds, as much as you are able without exceeding what is recommended. I would often rotate between ibuprofen and acetaminophen every two waking hours, taking pretty significant doses, until the symptoms were totally gone. Make sure you take this injury seriously, and you should be able to knock it out in a few days, versus living with it for weeks or months and having it negatively affect your performance.