Potential "unique" knee issues-can you help?

Please do a quick read and help me out…

Did an IM at B2B in 2010 (yes last year) and developed pain behind my knees on the bike. I rode the final 35-40 miles with a nagging pain but pushed through it cause I had to finish. Did the run and my “knees” (remember, behind them) didn’t really bother me as much at first, but was forced to walk for about 8.5 miles. Then run/shuffled/walked the rest of the way.

Next morning I couldn’t straighten my left leg. It was swollen from mid thigh to mid shin. It was that way for about a week, but got better each day. Went to doc a month later and he said try to work out and see if it still bothers me…didn’t work out, cause it did bother me-just from walking. I was told it was most likely a baker’s cyst that had burst whileon the bike and I just made it worse by running afterward.

I ended up taking off the whole year (very frustrating) but I still have issues when I ride (road or tri or mtn). It isn’t painful, just nagging, but it is right behind my knees in the crease. I am uncomfortable working out because I “feel” something is wrong, but try to push through the pain. I guess the only way I can equate it is riding and being bothered by your taint or a sore that causes you to ride with less power and determination.

Is it possible it is something other than a baker’s cyst? Is there something that could be off with my fit? I still feel the “issue” here and there when I am at home, walking, occasionally running (but it doesn’t bother me as much when I run?!)

I would like some help, because I felt going to the dr. didn’t do me any good.

Is it possible that I have developed arthritis (now my actual knees ache and bother me when I don’t even do anything)?

Thanks for your help.