Most likely this is being caused by the Safeguard Buffer (SGB).
This is a feature that prevents a user from selling his or her last item on both eBay and Amazon at the same time. You will need to have a greater quantity at Amazon then your SGB value.
You can view the SGB value in the 'Fba Inventory' view. Search for the SKU and click on the item to view a popup window. Please hover over the blue ?'s for better description of the SGB. The SGB can be changed by clicking on the value in this popup window.
If you only have a quantity of one at Amazon, you will need to change the SGB to 0. A value of 0 basically turns off the SGB. This will cause your eBay listing quantity to follow exactly what you have available at Amazon. Just be very careful not to sell your last item on both platforms at the same time.
We normally revise eBay listing quantity within an hour or so.