We just upgraded a 1.3.8a to .9h - and it's happening with us as well. Checked every setting, have 13 in stock, stock check level is 1, and yet every order we get an email.
The interesting thing is that it's saying stock is ' -1 ' ...
Was there a fix or a place to look for this one besides orders.php?!? (which I'll check in a moment...)
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