FileMaker should be "flashing" the last layout selected before the file was last closed on a local copy of the Database file. This is not desirable, but I get the same "flash" here in FileMaker 12. Take the file down off the server and open it with FileMaker pro. Navigate to the window you want as the last layout open. (I use a blank screen the same color as my initial screens to make this all but unnoticeable.) Make sure that you have removed any scripts steps from an OnLastWIndow close script that changes to a different layout. Close your file and put it back up on the server.
See if you now have an acceptable result when clients open the hosted database.