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I think the problem is probably caused by the script running while on the wrong layout. It sounds like you changed it to do Perform Script on Server which doesn't know your current filemaker client's context. If you put a go to layout at the top of the script it should fix your problem.
When you run a script on the server, the server opens a brand new connection to the database then runs the script. This means that the layout that the script is on when it runs is actually the layout that you are on when you first open the system. Also keep in mind that the new connection will also run the on first window open script trigger.