Take a look at this and see if it fits your symptoms: http://www.coolrunning.com/engine/2/2_5/194.shtml#runknee.  I am going through a bout of this right now myself.  The main thing seems to be to strengthen your quads.  The article includes some exercise suggestions.  It seems strange that the pain doesn't show up for two days but that is the same thing that happened to me.  I ran on Sunday, took Monday off, and the knee started hurting Tuesday morning.  Ice it, work on the quads, maybe take a few days off.  Good luck.

Len

I hope you will also look at this;

http:/http://orthopedics.about.com/cs/patelladisorders/a/chondromalacia.htm

This is what I suffer from...and oh BOY is it painful! 

http:/http://www.webmd.com/pain-management/knee-pain/runners-knee

  If you read the first link I posted closely, it generally strikes women over 40, who are otherwise healthy who have begun training for longer distances like 10K or Marathons.  JUST WHAT I WANTED TO HEAR!! LOL...

2nd the hip strengthening.  I'm dealing with it too and that is what my PT is focusing on, hip excercises.  For what it's worth I'm male and about to turn 35 so not exactly the typical patient but maybe close.  I have a pop sometimes when straightening my legs which is a telltale sign.  Does the pop eventually go away or are the treatments mainly for the pain?  The cool running article Len linked says something to the effect that chondromalacia patella is easy to treat but other sources seem to imply otherwise.  It's a little confusing and I'm not sure what to consider recovered: reduced pain, no pain, no popping or clicking, or just rest a month or 2 then learn to deal with it.

I am training for a half and think my knee is going to interfere big time. Ran last Friday and upped my miles to 5 from my typical 3. I try to run 5 times a week. Had some pain after that run in my knee but below the knee cap only on one side (inner). Took a couple days off and ran yesterday for 3 and can now barely stand up. Once I am up I can walk and it feels better but after sitting for a while it is super unstable and painful to stand up on it. Have been reading any and all articles on it today. So  bummed. I am scheduled for a 5 mile run on Sunday. Do I dare try to walk it? Would that be a big mistake? I keep thinking I can will this pain away but do not want to have to stop running. I am 56 and have only been running for 2 years. I love it.... Any suggestions on how long it will take to heal up and be able to run again appreciated. Heavily invested in race fees right now.