injuries like this suck...i think time should fix this. as long as nothing was fractured, your knee is probably just slow to recover. i've found that biking puts stresses on my knees in places that don't really get worked just walking around. i've suffered from knee pain in the past which was only when i was on the bike. i just had to be deligent about streching (before and after), keeping my form in check, and just waiting it out. take it easy and when you notice it starting to hurt, call it a day and try again the next time.

also, unless it's absolutley necessary, try not to take pain killers. just listen to your body.