The Canadian shopping cart is a little buggy. (That came out more apropos than intended. Sorry.)
Send your customer an invoice through Paypal 'Send Money' for all his items. There is an invoice form available. Note that the invoice is for all the eBay transaction numbers. You will also be able to bill for the multiple purchases.
Then when he pays, mark the purchase as paid manually.
The customer is covered by the Paypal Buyer Protection which is pretty much the same as eBay's. You are also covered by eBay.