Yes, Updater and Monkey are separate programs. But (afaik) Monkey does not call on Updater to finish. Monkey should install the firmware itself. Updater replaced Monkey for future products at some time in the past, but they never worked together.
Please describe exactly what happens, including screenshots if possible, when you run Monkey. At what point does the update process fail, and why do you think it’s trying to call on Updater?