I spend a lot of time on Ebay with heavy equip. and machine tool stuff. I've seen the same thing you describe, but not often. When it does, I think it is more due to a winning bidder that won't follow through with payment. Then the seller has to re-list the item. I saw the same South Bend lathe sell twice recently.
If it was shill bidding and they ended up buying it on a troll account, the seller would have to pay the final value fee and a re-listing fee. The whole idea of shill bidding is to get someone else to pay more for the item, not end up buying your own item.
The other thing that happens is sellers making a side deal and ending the auction. Not really the most fair way of treating your customers, but I've done it too. Sometimes it's a case of "bird in hand" vs the unknown.
I usually set the minimum bid at the absolute lowest I'll take for the item. Yeah, you get more bidders starting at .99 or whatever, but then you need to put a reserve on it or risk it going for the minimum bid if there's only one bidder.
It's a fun game and I'm sure there's a lot of ways to cheat. Overall, I think shill bidding is the least of things to worry about on Ebay.