Woo Commerce first changes status to Complete before it changes to my Custom

The problem I have is that when someone pays online through my store Woo Commerce first starts the order status as Complete then Custom Order Status changes it to my custom status called Payment Complete. The issue I am having is I have a plugin that thinks if the status in Woo Commerce changes from Complete that, the order isn’t actually complete, and it reverses its functions. Why doesn’t this plugin bypass first changing the status to Complete since the custom status I set should show it as a closed order?