I am going through some knee pain right now as well, but got an MRI and turns out my fat pad below the patella is getting impinged In the joint. I would get short bursts of pain and depending how bad the impingement was, the pain would go away fairly quickly to lasting a few hours.

Sounds like yours may be different though.

My doctor at first said we could do an injection and see what happens, but I didn't want to do an injection without knowing what was going on, so I requested an MRI. Now we know what we are treating.

I'd recommend an MRI to figure it out.