PaulS:
I still don't quite believe this but the documentation for 1.0 sounds like the pullups are not active for pinMode(INPUT).
They are not active by default. They can be activated, using digitalWrite(). Or, the call to digitalWrite() is made for you if you use the type INPUT_PULLUP.
Whew, thanks.
I think that the "disabled" in that sentence refers to the fact that there is now a call to digitalWrite() in the pinMode() function. It is called with HIGH or LOW based on the use of INPUT_PULLUP vs. INPUT.
A peak at the code confirms this. The digitalWrite() function isn't actually called, but the equivalent register manipulations occur.