We remove it from one listing and tell him to buy it but don't pay so we can send invoice with other five added as 'additional charges' - We have done this ten times? with no problem. I know you have a blurb about contacting you before buying/paying for multiple items on your listings, but how many actually read it before buying and paying causing you to have to refund some of the shipping cost? After all, the info is not titled Combined Shipping, its header is Because of the way ebay works, which most buyers do not care about and are not likely to wants to combine shipping on six fixed priced things that have immediate payment. People do not often change their minds about those type of items, or find them for less, so why have IPR to begin with? If people are buying multiples and paying immediately, you are losing the fees when you refund shipping overages. In my experience rarely do I have payment issues with vintage or collectible items. In going over your profile I see you sell mostly vintage collectible items, some of which you might definitely sell more than one of.
Only reason I can think of why the payment went through is, the buyer gave you the wrong item number so the IPR option was not removed from the piece they actually were going to buy.