My official policy is that the purchases will be sent separately, though in practice things are a little different (I mainly have this as my policy as it means people can't really complain if I do opt to post separately - eg if it's cheaper - and also I would occasionally get people buying other things hours apart, after I've already packaged [sometimes posted] earlier purchases and wanting combined postage).
Usually, however, I automatically combine and like others, refund excess minus additional costs incurred. Sometimes I will upgrade the postage, to registered or parcel post, but I still refund a small amount as a courtesy gesture, since often times if I upgrade postage, I would have anyway if the buyer had paid for them all together and paid my lower flat rate P&H instead, plus I still get the benefits that come with the upgraded postage like tracking etc.
Very few acknowledge this in one way or another. Every now and then I get a really ticked off message because the buyer thinks I refunded for being out of stock or something (I make a note on the refunds what they're for, but don't advise the buyer in a separate eBay message or anything so some will just see the refund notification and go off), and, even rarer, I'll get a message thanking me as they hadn't thought or expected postage would be combined. How much I actually refund depends on postage costs, whether I upgraded etc, but I try to honour my normal postage discounts as much as possible.
One thing I do want to mention, is that sometimes a buyer will make a single payment, but it gets split by PayPal into separate payments. One reason this occurs is because there are different postage services selected hy the seller. For example, if on one listing they have "Standard postage" selected, and on another they have "Parcel Post" selected, the payments will be split because in eBay / PayPal's infinite 'wisdom' each item is being posted by completely different services and can not be combined (for this reason, no matter whether I'll be using large letter or parcel post, I use 'standard delivery' and just quote the price, which also means my automatic postage discounts will be applied in the shopping cart).
This also happens on multiple-item orders where different postage services are available and the buyer switches only one, thinking it applies to all, when unfortunately it doesn't. eg I have standard, registered and express available. If a buyer purchases 5 items and during checkout, selects express on one item, I'll get two payments with the full amount of express charged and paid on one item, then standard postage charged and paid on the rest. I always combine and refund in these cases too, and usually refund the full amount of the excess postage (there's a few reasons why I treat these a little differently - one being that my standard postage rates are actually a little under what I should be charging while my express charges are not, and also because when express is paid for, some of my risks are minimised).
I try to advise people in my listings how to access my combined postage discounts when using mobile apps etc, as that helps us both out, but it usually goes unnoticed unfortunately, unless / until we have direct communication via messages.
