I think I have been having the same thing. In the MyEbay section of selling manager the number (next to active listings) would drop every now and then. I have lost about 20 items over about 3 months.

The  other stats like open cases, etc....randomly change all the time. I thought it might have just been a false number but when checking active listing through search it comes up with the same number.

At first I thought it might have been the listings with zero quantity (still active as I selected that in options) that have been sitting for a while. I assume ebay must delete them after an amount of time.

I actually had an email from a customer recently asking if I had an item and to my surprise the listing was gone, plenty of stock. So they are definately dissapearing.