Assuming you had the new bike properly fit...

Where are you, gge?? If you're in CA, you may want to consider a trek to UC Davis for biomechanical testing. They even have a specific fitting for bicycling (see their website here ).

If you're not anywhere near Davis, I'm sure other universities with sports medicine programs have similar services. You can also get these services through the provate sector, but I can tell you form experience that it's cheaper (and just as good) to go through a university.

I went through biomechanical testing almost 3 years ago for running related woes. I highly recommend it; your knees aren't something to mess around with. Seriously. Listen to the woman that waited too long to do something seriously about it, and is still paying the price 3 years later!