Dave- The bones in the knee are covered with articular, or hyaline, cartilage. Along with articular cartilage there is meniscal cartilage (in the menisci, which act as shock absorbers at the top of the tibia), and fibrocartilage, or scar cartilage. When functioning properly, articular cartilage and joint fluid act as a lubricant and reduce friction. Articular cartilage helps the bones glide easily past each other during knee motion and serves as a thin protective layer to the bones it covers.
Articular cartilage is fairly resilient but does wear down. When it does break down, the condition is known as degenerative arthritis (arthrosis). Since hyaline cartilage has very little blood supply it heals very slowly or not at all.
The body's nervous system is brilliant and alerts you that something is wrong. However, articular cartilage does not have pain fibers and, as a result, pain signals come from other tissues being irritated from the cartilage injury. Therefore, it is possible for the articular cartilage to be damaged without you noticing any pain. Small aches and pains, or swelling in your case, may be the only warning of articular cartilage injury. The symptom of knee swelling may be a result of stimulation of the bone fibers under the articular cartilage or irritation of the fluid-filled lubricating sac in the joint (synovium).
Another symptom is "cracking" or "crunching" sounds as joint is moved through range of motion.. sound familiar? If you have loose debris in the joint you may eventually experience a catch or lock-up of the joint.
There are two things you can.. go the doctor and get an MRI and find out what is actually happening rather than ask some schmuck you've never met :) Expect her to tell you to stop running then ignore her. Most smaller hospitals don't have the ability to routinely make substantial diagnoses of articular cartilage injury with MRI alone. X-rays may also help your doctor to indirectly diagnose cartilage injury. If they do find a problem then there are several ways to go about helping the issue.. but probably nothing you would consider a true "fix". Our bodies simply wear out.
Or you can continue on until you start to feel pain, then deal with it. I would tell you to start a weight training routine that will help strengthen your knees- leg extensions and hamstring curls using light weight to start with. This will help provide strength to support your knees more effectively.
You may also benefit from orthotics to help with any foot plant imbalances that are causing undue stress on the knees.