Replies aren’t showing up – misplaced comments also

Hi,

I am not sure if I am in the proper section to do this.

but , replies aren’t showing up like they supposed to and we have discovered the comments are misplaced.

I searched the forums for similar problems but I can’t find any or atleast a solved thread.

Anyone can help me? our site has a very high live traffic and community and we can’t just like do “try switching to twentytwelve theme”. I am a techy person myself and I am very open to any insights. Thanks a lot!