I tried to retrace your data as far as possible. My experience with vaccum-Caps is another, then your data show. I believe, that you have some slip in your actuation. I did a little calculation for frquency per step and saw several glitches: i.e. from 14.125 to 14.150 are 8.704 steps, also from 14.2 to 14.225 you have documented 1.416 steps. There are some points more.
Is it possible, that the drive-shaft turns loose sometimes or you go with to high rpm, that the stepper looses steps (glitches)?
The vac-caps are normally linear from maximum C down to 5% of C. At the last part (min C) there start, depending on construction, non linearities.
If your cap is NOS, it is also possible (and normal), that the lubrication of srew thread has got old and stiff. You should renew the lubrication.
And yes, the controller makes a linear interpolation of the steps between two stored values to get the value for a not stored frequency. So you have to take the more programmed steps, the nearer to the minimum of cap.
So take a look to your system.