I'm now working on this the last 6 hours...
i made my own theme in witch i used the comments-popup.php file (inserted with ajax using fancybox) to write comments on posts and pages.
since the upgrade to 3.0.x my theme returns a 404 error if i try to load the comments-popup.php on a page, but works on every post.
after some hours of searching, i'm comming to the conclusion that the problem is within the wordpress chain, wich in some point retunrs a 404 instead of the processed content of the popup file,
i'm having the same error using the default theme (inserting comments_popup_script and comments_popup_link funtions)
if anyone want to see what i mean, look at my site http://www.andresbott.com
->in "mumuc" (page) you can't write a comment, but on every blog entry you can.