Ok i have setup the basic BuddyPress forum site and have not done any visual design or site structure things yet, but everything is working fine with BPS installed together with BuddyPress and bbpress.
this is a new comment reply
forum.ait-pro.com/hello-world/#comment-2
this is a reply to an old comment
forum.ait-pro.com/hello-world/#comment-3
this is a group that i created and tested a comment reply and no problems
forum.ait-pro.com/groups/test-group/
And i just noticed this - your comment reply has /?#post-47 instead of /#comment-3
vegeangel.com/groups/vegetarian-recipes/forum/topic/spaghetti-bolognaise/?#post-47
I just thought of something really obvious - do you have more than one BuddyPress installation on your site?
this seems odd to me /groups/vegetarian-recipes/forum. is this forum another BuddyPress forum installation or is the just the path you decided on the only BuddyPress installation is on this site /vegeangle.com because i guess it would be possible to install another subfolder site in a folder called /forum. or maybe with BuddyPress you can have nested forums? i am not a BuddyPress expert so i am not sure what you are doing.