The order of pinMode and attachInterrupt matters. If you use pinMode and then attachInterrupt, attachInterrupt will overwrite the PULLUP condition and put the pin in a HIZ state and the pullup resistor will not be enabled.If you use it the other way around, as you stated, everything should work correctly since the pullup resistor will be enabled.
Thanks for the input. I figured out that the order matters, but I didn't see it documented anywhere. I have verified that the non-Intel Arduino platforms do not have this behavior, and they seem to work fine if the pinMode is specified before attachInterrupt. I figured that there was likely a document/wiki somewhere that detailed the differences with the Intel Arduino libraries so as to allow folks to port over code easily, but I have not found one.