I have done some testing with this and it seems that whenever I create a button on my live PayPal account and it is in the My Saved Buttons area it will appear in the list of available buttons in the tool. I did notice that I had to close and re-open ExWeb to get the list to update, but after this the button was available and I was able to add it into my page.
Can you see your other buttons that are in the My Saved Buttons area? Is the problem only for a specific button? Please post back with some more detail about this and include the steps you are taking to create the button on PayPal that is not showing in the list.