Isn't the volume in question the volume occupied by the gas, not the volume of
the chamber? As others have said, by having just a few molecules, you're not in
a thermodynamic situation any more, and these two concepts are no longer the
same thing. By moving the piston when no molecules are hitting it, you are not
changing the volume of space occupied by the gas. Ultimately, I agree with the
other posters -- you're applying macroscopic concepts like pressure, temperature
and volume to a system where they don't apply. Hence, the paradoxes.