Filemaker will run the script that you have selected with the script trigger OnFirstWindowOpen which is set from file, file options, script trigger. This script may go to another layout that has a script trigger on it and since it is going into find mode it has to complete before it continues.
Open up generic FileMaker, open the script debugger, then open your db to watch what happens.
I've noticed the screen will flash on the last layout used if I close the DB with the 'x' on the main window, instead of closing it with a button and close file script, from the 'correct' layout. I wonder if It's possible that the find script is performing because the last layout you used the last time the db was opened contains the find script, and this 'flash effect' is causing it to trigger. If this is happening, make sure when you close the database it's closed from the same layout it was opened from with an OnLastWindowClose script trigger.