Hi Josh,
I've never used Alignmaster but I did have a similar issue once with my own mount. In my case, the solution was to reset the mount to factory defaults and re-enter the geographical co-ordinates, GMT offset and local time.
Since you're getting those values from EQMod, it might pay to double check them just to be sure. Without the hand controller I couldn't suggest a way to reset the mount to factory defaults, though.
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