I can't find an answer to this question, so maybe the community can help me.
I have a multi-site install. Custom modules enabled in my specific-site install are appearing on my main site.
I cannot see this modules in my admin/build/modules page of my main site, but i can see their code is running in the main site (specifically, they are running hook_link on the comments). I read this post and it appears that I have my multi-site setup done correctly. This is how my directories are structured:
Main site:
sites/all
--- themes/
--- modules/
Sub-site:
sites/sub-site.com
-- themes/
-- modules/
---- custommodule/
I have multi-site set up with these configuration options:
$db_prefix = array(
'profile_fields' => 'frontend_',
'profile_values' => 'frontend_',
'comments' => 'frontend_'
);
should there be another configuration option for a modules table or something?

Comments
Only way you can have this
Only way you can have this happen is if you're sharing tables across installs. It could (total speculation) could be that you've got the comments table shared; this will reference something like node 5 has 3 comments but the node 5 it's supposed to be talking about is a different site the the current one you're on. I wouldn't share comments across sites unless you have a reason for doing so as this could cause a conflict. As for firing off hook_link not sure, maybe there's some other module running _link that looks at the comments table for entries w.o. checking for the module first.
Again, purely speculative.
Ex Uno Plures
http://elmsln.org/
http://btopro.com/
http://drupal.psu.edu/
I am sharing the tables
I am sharing the tables across installs, but that isn't exactly the problem ... the comments table is prefixed. So I don't have a problem with ACTUAL subsite comments showing up in mainsite articles (and vice-versa) but rather the manipulation to the links that subsite modules execute are showing up on the mainsite.
Does that make sense?
Do I need to prefix my modules table, or something?