There is no known bug that I know of that matches what you describe and this is a script that I frequently use in my own systems with no trouble. I recommend:
a) Launch FileMaker without opening this file
b) enable the script debugger
c) Open the file and step through the script performed by "on first window open".
This should allow you to watch the above script hide the tool bar and you may spot a clue in seeing exactly when the tool bar is brought back and by what.
I have done as you have suggested. It appears that another script runs after the Scripttrigger on firstwindowopen has finished. I have no idea how though as the layout has no STs on it.. What could cause this script to run? Do you have any ideas?
If you watch very carefully, the script debugger should show you the name of the script trigger at the bottom of the debugger window. That could be a helpful clue here. It's possible that the script trigger is being tripped when your OnFirstWIndow open performed script exits another layout. A change in layouts can trip any one of a large number of triggers on either the layout being exited or the layout being entered.
I'm sure you checked this, but don't forget there could be an could also be an 'OnWindowOpen' Trigger too.