A little hard to suggest anything from the info in your original post. A bit more detail might help.
"I have a script that checks the persons login and password on startup. You are presented with the first layout with buttons that are non-working.Once you login it takes you to the authenticated screen which is a duplicate only with working buttons."
Sounds like they have to log in twice. Once when they open the file and then a second time from the "non working buttons layout". Why does that happen? What scripts are you using here?
True, and actually the login script doesn't log them in as much as set some variables and check what system the file is opening on (i.e. iPod, iPad, iPhone, Desktop Computer) and then choose the appropriate layout. For example it would be a much different layout for FileMaker Go then it would opening on the traditional desktop filemaker.
I think I figured out my issue but soon as I get into work I will post snippets of the code to see if that helps.