Exchange Servers in Multiple sites

I have just inherited a problem from a previous systems administrator with Exchange 5.5.

There are 8 distinct exchange sites in our organisation, each with their own servers, being BDC’s of our Primary site. It all works fine apart from one thing.

Two of the remote sites servers are also listed in our Primary servers local site, as well as in their own sites. This means that e-mails are getting very confused and generating a huge amount of internal RPC traffic. The mails get there, but can take up to a day.

I am at an initial loss as to how to fix this, and I do not want to start again with the remote sites.