For some reason on my dedicated server any site other than my main site keeps reading the wrong cgi-bin.

In other words site A cgi-bin is being read by site B instead of site B reading its own cgi-bin which has been setup specifically for it.

Anyone know what could be going on?

Now the main site A reads from its own cgi-bin but any other site tries to read from site A's too instead of its own cgi-bin.

Your httpd.conf probably not configured right.

Why dont you post the VirtualHost block of your httpd.conf here?

You probably do not have a cgi-bin directive set up in your VirtualHost. If you do not do this, then cgi-bin queries will go to the primary server's cgi-bin instead.

You should have a ScriptAlias directive in your VirtualHost section.