I've noticed that if you have a stack of 2 or more counters at game start, and during the setup phase, .. that the stacks cannot be moved to a new setup location.
.. they can only be moved one unit at a time. [&:]
That's by design. Theres a good chance you wouldn't want to move the stack too. We went with the single unit route. I can add a feature wish list item to allow a stack drag with a like a shift or ctrl key click for the programmer to review.