Most of what I'm saying below is speculation based on the material properties as I haven't ever machined teflon to high tolerances.
My first question would be if both of your pieces from the same lot of Teflon? Different lots may have slightly different internal stresses from the sintering process.
Teflon has around 10 times the thermal expansion of steel so if there was a large temperature difference, this would cause tolerance problems.
Based on the large variation that you mention, my instinct would be to guess too high a clamping pressure perpendicular to the face where material was being removed was used. Teflon has a much lower modulus and a much higher Poisson's ratio than steel.
In essence, a part that was heavily clamped would have expanded perpendicular to the clamping force during machining and slightly contacted in the plane of the clamping force. A part squeezed in this manner would be longer on the machine and shorter when the clamps were removed.