As of June 2016, certain fulfillment orders through Amazon FBA have started being assigned Amazon-internal tracking numbers.
For example these can be found starting with: "TBA" etc. These orders are fulfilled via "AMZL_US," which has no customer facing tracking system. This means JoeLister won't have the necessary data to satisfy eBay's demands for tracking upload, leading to a metric hit at this time in the "top-rated seller" metrics.
There is no easy answer to this. As of right now it seems we can only chalk this up to cost of multi-channel fulfillment, as Amazon has no need to provide proof through tracking, leaving the eBay-side of things empty-handed for these scenarios.
We are working on a solution, but as of now it seems everyone will have to take the metric hit. We are in communication with eBay about this at this time.