See, I got a basic fit when I purchased the bike. It was actually pretty thorough -- it took him about 2 hours and he didn't charge any extra for it. He put shims in my cleats, and measured my knee position with a bob, and watched me walk to see what my gait was like. He said they did have a professional fit (the one I am considering), but that it would cost quite a bit. After getting back from the shop, on my first ride, I immediately noticed some pain in the top of my calves which was fixed by lowering the seat about 2 cm. And then over the next few months, the lateral knee pain developed.
He said I could come back within 6 months of the bike purchase to get some quick fit adjustments, but I don't know...
I assume the professional fit he is talking about is one where he took a training program. I shouldn't put the blame on the fit though -- I guess professional fits work for most people and it's probably just the case that I have a strange body that is immune to attempts and relieving pain.