I think that I may have fixed it. Here is what I did...
The database seemed to have some sort of corrupt setting or something, so I created a new database with a copy of the out of the box Imperial database.
I then went into my database and exported all my materials, seams, connectors etc.
Then in the new database I imported them all. This along with the setup of my machines basically got me a clean database without the duplicate connectors issue that I was experiencing. The problem now was that I did not have user level access control like I wanted. That was a simple matter of copying the "users" folder out of the old "database" folder into the new "database" folder, this added the user level access control and made a new clean database that did not have the corruption from before.
Mariah, thank you for all the work you have put in on helping me with this issue. I am not sure if you are wanting to keep chasing this and see if you can pin-point where the corruption was in my old database, but I am going to mark this as a solution. I would be willing to help you if you want to keep working on it though.
Thanks again!