A small update, we ran another tool that is a cold runner with the same shot size but different parts. No color issues were observed with this mold, but some processing changes were made that will hopefully translate back to the tool that was having issues.

After talking to Reiloy we are using a pretty severe reverse heat profile (410 front zone, 460 rear zone).
We installed a mixing nozzle body with four twist elements from PPE.
We have started mixing the liquid color by essentially rolling it around the shop before use.

Some additional steps we tried that did not help:
We tried using the smaller screw that was designed for mixing acetal and saw worse performance, possibly due to a short residence time of about 35 seconds.
We varied backpressue from 300 to 5000 psi and screw speed from 30 to 300 rpm.
Attempted various ways of feeding the liquid color into the material path and premixing the color with the pellets.
Mold Masters has not provided us with any technical support but has sent us all drawings of the hot runner system.