[iNik]

Open up your default document and run this script:

tell application "OmniFocus" to tell default document
make new document window
close result
end tell

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.

[Brian]

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