First and foremost - proceed with caution. I have a thread in the "Rider Wellness" forum at this moment going, asking for advice on how to deal with torn ligaments in the knee. While mine was a freak accident in an English saddle, if I had taken the time to build my body and muscles up before riding, I could have avoided the problem. I tore seven ligaments, in each knee, at the exact same time. It was excruciatingly painful and it has kept me out of the saddle for two years(plus, as I still have to figure out how to get an MRI paid for and then physical therapy). So yeah. Proceed. With. Caution.
As for specific reasons regarding why your knees hurt - I'm not a doctor, I can't even see or feel your knees, and I don't have any guesses to offer you. I would say that you can fall out of *riding* shape relatively quickly. If you take two weeks out of the saddle, you can get saddle sore on your next ride, even if mildly. Your muscles will still exist, but if you don't use them they gradually go away.. especially if you're not using them as much as you used to. From experience, I'd tell you to start working on your core muscles, your buns and your thighs, and relative knee strength. (For me, it's apparently walking up stairs, without any professional input.) Swimming is a great way for an over-all body work out.
But, I'm not a doctor and my knowledge is limited. All I can really do for you is to tell you to follow the advice you do get and be careful not to get hurt. Good luck.
The path is different for you and me, but the journey begins in the heart.