Scooters rock, and I speak as a Ducati Panigale (899) rider. For city commuting my SH125i is all i need, its a blast to ride and filter with although I do feel an arse riding it. I just tell people if it all goes tits up work wise I can get a job delivering pizzas.
With regard to seating position, the problem I see with the PCX style is that it makes you sit back on you cocyx, so puts pressure on it, potentially exacerbating the problem.
Simple thing to try first (although you might look a t!t), pull your feet back a little, almost to the pillion pegs to force your body angle to be more upright/forward rather than reclined. Not a permanent solution, and might give you knee ache, but it will tell you if you can improve the position, or just inform you that you need a different riding position.
I'd agree the SH is a more upright riding position and might be better, but would try to change your position riding yours to see if it alleviates the pain, then work out where you go from there.
RBW.