This seems to be new in the one magazine I moderate. In some threads, but not all, I can't see any comments, but I can see how many comments there are, and when logged out I can read them. I can go to another instance and see them there, so I also know they're federating. Very odd.
I thought it might be something to do with threads started by users from other instances, but there is at least one of that type where I can see the comments fine. I also tried turning off my *monkey scripts, logging out, and clearing cookies. Nothing seems to help.