Hi Cody,
Assuming your Kettle Boil is sufficiently robust, I doubt you have a stratification issue.
I suspect your hand-held refractometer is the issue.
The sample volume is so small that even a small cross contamination from the previous sample or sample evaporation on the prism can throw off your reading.
Make sure that you rinse the entire sample surface including the cover plate with fresh water. Then, using a soft tissue, wipe off all surfaces until completely dry before next sample.
Then, the sample itself can be problematic. You are pulling a boiling wort that will continue to evaporate and thus concentrate in the refractometer. So, you either need to let the wort cool a bit before placing drop in device or be very fast AND CONSISTENT when placing drop, closing cover and reading. A deviation in this time will affect evaporation and thus your reading.
Cheers,
Daniel Carey
New Glarus Brewing Company
------------------------------
Daniel Carey
Brewmaster
New Glarus Brewing Company
New Glarus WI
(608) 527-5850
------------------------------