I am posting this as I have found the answer and want to save everyone the frustration.
There are 2 seemingly identical "ebay" storefronts now. So any automation rule that used the marketplace filter and ebay as that marketplace will need to be edited to the new "ebay" marketplace. Got to your automation rules, select edit by the affected rule. From the dropdown in the filters simply select the "ebay" below the ebay FR and save. The "ebay" above ebay AU is the old integration.
This solved so many problems, I hope it does for you as well.