Same thing here, only I'm using the original loop. But I noticed that the links display fine, if I do not use any other shortcode plugins in the post/page.
http://www.streathammarlboroughcc.co.uk/index.php/home-test/
As soon as I insert another bit of shortcode from another plugin (i.e. Recent Posts Embed, Composite Post or ggis Inline Post) the links are not showing properly, and the shortcode is seen instead.
Needless to say that I am using the latest version, and that I tried quite a few combinations. All without success.
I like your little plugin and it's quite unique. So I'd really appreciate a solution if possible.
Thanks!!