This is the same issue I have had with some of my buyers.

Until a couple of days ago, I thought they were doing something wrong, but I had the same problem as a buyer the other day.

Had two items in the cart from the same seller, both had identical postage costs, combined them into a single transaction and paid in a single transaction, but after I made the payment, the purchases separated out into two individual transactions.

Obviously there must be a glitch in the eBay system. It now also separates purchases if there is a difference in the item shipping costs, something it never used to do, though I am not sure if this happens with everyone. 

Very frustrating for the seller. There is the option to add the same tracking number to separate transactions to combine the shipping into a single parcel, but it is cumbersome and the postage refunds mess with my record keeping.