If you use a 3rd party module to update stock or order status then it is very likely that this will not be updated to Etsy.
Most developers integrate with the database directly which OpenBay Pro cannot pick up the changes to. This is not a bug or flaw with OpenBay Pro, 3rd party developers need to ensure they trigger the events system when a product or order is updated. This is available in OpenCart from 2.0+.
The events system will trigger OpenBay Pro to pick up on the change and update the stock/order accordingly.