I would start by speaking with the fitter.

As Luna mentioned fitting is at least to some extent subjective; it is also an artform not some pure science that works for everyone the first time.

I imagine your fitter will have suggestions/modifications based on the increased knee pain, and I suspect those suggestions should come free of charge (he's already gone through all the efforts to get your flexibility, issues, on bike measurements, etc and ultimately it's in his best interest for you to be happy).

It may take a few iterations to get everything *just so*.

I just had my first full on professional fit for general measurements (stop motion camera, size cycle, range of motion tests, medical issues, flexibility, fitness, cycling goals, the whole 9 yards (it took more than 2 hrs)). The bike that comes out of that won't be here for a few months, but I have every confidence the bike will fit wonderfully. The same fitter has done "to the bike" fits for me for both my road and mountain bikes (that I bought from him). We've made tweaks since those initial fits (cleat position, spacers added/removed, minor saddle fore/aft) even though I've had no major complaints. The tweaks were mostly initiated by him rather than me actually. He's always asking me how the bikes are feeling, if anything is hurting, if I feel like something needs changed, etc. I guess that's the benefit of having a really great bike shop and riding with their club as my fitter sees me ride often. He's never taken a "well, this came up and this hurts now" comment personally, just tweaks it and has me report back in a week or so.

So anyway, I think my point is two fold. 1) Don't be worried about offending him (because while I'm sure he's not expecting/wanting you to come back miserable, he should understand that it happens sometimes and be more than happy to adjust things for you based on the new issues or work you towards the fit in smaller increments if it's a matter of doing too much too quickly). 2) Don't be discouraged quite yet (it may take a few tries to get it perfect, and even then fit is dynamic as your body/fitness changes)

Or, in sort, Luna pretty much nailed it.