Im running Wordpress 3.1 and it is showing that you will find comments (ie: 3 comments) however when you click in to the single blog publish they do not appear however the comment form seems.

I am not sure be it a template problem or something's not correct within the functions.php.

I've the multi site function running for multiple blogs.

Other people getting this issue as well as possess a solution?

It needs to be template problem, make certain you have comments.php file contained in your theme directory. You might want to copy from default theme too. The functions.php is not related to that though.