In the end it was all my fault. I had added a comment count to the 2.0 and Atom RSS feeds thinking it would give people an idea of how busy a particular entry was, but apparently this may have been triggering the multiple listings for entries in some readers. Thanks to Boris Mann for pointing out my mistake to me. Here I was thinking I was being helpful and all I was doing was making a mess of things. 
Stupid Evil Bastard
What the fuck is wrong with you people?
I was going to mention that, but I’d already bugged you about the entry author and didn’t want to sound pushy 😀
…that, and I figured I was in the minority, using RSS feeds…
Never worry about bugging me when it comes to problems with the site. I’d rather hear about it so I can fix it.
Good to hear that I wasn’t just imagining the weirdness. Thanks for looking into it Les!