On Windows, you may have to use SAT4J instead of MiniSat. In order to do so, you can set or change the appropriate flag for autotool-capabilities under flags in the relevant stack.yaml to true. Thus the section might look like this:

flags:
  autotool-capabilities:
    alloy-use-sat4j: true

Or provide it as an argument to each call of stack, e.g. stack build --flag autotool-capabilities:alloy-use-sat4j.