You could try taking evening (or dawn) sky flats first on one side of the pier, then after a flip and then back on the other side of the pier.
Differencing the resulting flats would give you an indication of their repeatability.
I've had similar problems with flat calibration in the past on the Issac Newton Telescope (in a previous life when I had access to big scopes), we spent a lot of time trying to track down flat field errors and in the end put it down to scattered light upsetting the flats. Flat fields can be a right pain, best to avoid the meridian flip if at all possible.
The only other though that I had is whether the star PSF varies significantly as a function of field position. If the photometry apperture is relatively small then there could be a significant difference in the amount of light outside of the apperture depending on where the star is in the field. An 'apperture correction' is often used to overcome this problem, particularly with systems with strong coma or field curvature.
Cheers,
Darryl