You're not the first person to report having issues keeping up the fan speed with an 9800 card, don't know if 'the problem' has been run down yet. Seems likely a driver issue. And YES, fan speed ABSOLUTELY affects your max overclock on these cards, I strongly suspect it's because the memory heats up, and the mem chips have no sensors on them, so you have to manually crank up the fan.
BTW, you *are* setting the fan speed in the 'low level tweaks' section, not the 'system tweaks', area in RT, right?
The problem *could* also be that not all 9800GTX's use the exact same memory chips, and hence, some of them are going to overclock higher than others. But I don't know that to be the case, it's something you'd have to research probably. If it makes you feel any better, the difference in FPS between 1100 and 1200MHz on the memory clock is going to be so incredibly miniscule that it's probably not worth worrying about