I stumbled upon a problem when I switched to IDE 0022:
analogWrite is now incompatible with 9 or 10-bits PWM.
suggestion is to implement multiple PWM modes (higher bit resolution, different prescalers, perhaps even different PWM modes -fast vs phase correct) in the Arduino code.
Default settings could be what it is today, but it shouldn't be too hard to implement a few switches for advanced users.
analogWrite is now incompatible with 9 or 10-bits PWM.
Are you on a MEGA? The normal arduino only has one 16-bit timer; I don't see how the 8 bit timers are supposed to support 9 or 10bit PWM.
In any case, changing timer modes and expecting the predefined functions that use those timers to continue to operate correctly seems ... overly optimistic.