You don't give us a whole lot to work with, but here are a few things to consider...
Have you had your bike professionally fitted? If so, how long ago? EDIT: Reread the original post...do you have your old bike (that I assume didn't give you issues) to take measurements from? This is the biggest variable and I bet the root cause of the problem. I'd take it back to where you bought it (or got fitted if its different) and let them know its not working for you. If its a reputable shop, they should work with you to iron the issue out.
What cadence do you ride at? I find if I let my cadence drop even 10 RPM, it really bugs my left knee (the one I have had persistent ITBS issues with) after a few miles
Has nothing setup wise changed but you've developed a knee pain?
Did you ride while dealing with ITBS last season?
Part of the reason I took up serious cycling was because I wanted a high exertion cardio activity that was relatively low impact. I still run, but if I run too much, my IT band lets me know. I find cycling to help a lot. I have to be militant about stretching, staying hydrated all the time and keeping my cadence up while on the bike of ITBS kicks back in.
Last edited by Wescoe; 05-31-11 at 10:26 AM.
Reason: momentary lapse in reading comprehension...