Hey there,

I had a similar problem on my website, only for me all the links were gone. No more comments, read more, ... and so on
After doing some research i ended up on your site, i guess there's still no solution for your problem. I'm not sure if my problem was the same as yours but i had a module 'Synonym Collapsing' wich somehow removed the links on my site. Perhaps this might give you some ideas to find the solution for your website ...

Nice theme btw :)