I've heard from others that eBay have recently tampered with the set-up so that if people make the seller an offer then eBay takes their payment details and automatically takes payment if the offer is accepted. Perhaps it would be worth checking your settings to see if eBay has been tampering with your preferences behind your back, and change them back again to deactivate automatic payment if they have.
One other thing that you could do would be to include something in your listings along the lines of "If you would like to purchase more than one item please add all of your chosen items and pay in one go, as I can then send all of the items out in one parcel, using the same tracking number." That way it may help to stop people purchasing items on multiple listings and paying separately on each one.
In the event that eBay have tampered with your account and set it up to automatically take payments the moment a buyer commits to a sale deactivate the function so that it doesn't happen in the future. If you were to do this and it subsequently resulted in you being able to send invoices out to buyers who make multiple purchases you could even go so far as to include something in your listings along the lines of "A discount may be available for multiple purchases - please wait for the invoice before making payment in order to receive the discount" so as to encourage people to hold off of paying before you've had the chance to get the invoice sent out (that's if you're willing to offer potential buyers a multi-buy discount). If buyers notice that there's a prospect of being able to earn a discount on the overall purchase price then it may also result in more sales, too, which would not only be beneficial for the buyers in that they don't have to pay quite as much, but would also be beneficial for you in terms of an increase in overall sales per month.
