For eBay sales, note we can only process those when the buyer pays with PayPal, not if they pay directly with a card on eBay. Aside from that, the next most common reason we may fail to process an eBay sale is if the product's Item Name in E-junkie does not exactly match the item Title in your eBay listing.
If you're seeing completed payments in PayPal that don't show up in your E-junkie Transaction Log, follow the troubleshooting steps here to sort out the reason for that problem:
This help page covers how to test various aspects of your setup: