Scripting bug on "close window"
 

Open up your default document and run this script:
[INDENT]tell application "OmniFocus" to tell default document
make new document window
close result
end tell[/INDENT]
It closes every window. Not just the new one.

The same happens with a "close window 1". If I close windows behind the first one, (i.e. "close window 2") things work just fine.

I can duplicate the behavior. I'll write this up as a bug.