Hi,
To receive shipping costs through MyCostPro the two following conditions:
You need to be enrolled in the eBay Selling Manager program (free) and
You need to ship the item through eBay's shipping service.
It looks like you are in the selling manager program already since you implied that you have been getting the information normally up until recently.
Did you ship these items through eBay shipping?
If yes, can you email me your sales record numbers and I will investigate further!