I poked at this a bit, and my only suggestion is that perhaps it's related to either the Win32 apache or the Win32 perl you're using. I couldn't reproduce the problem on either of the unix servers I tried.

You might try adding a __WARN__ handler. Find out if warn() is actually being called twice or if it's some issue with stderr being duplicated. E.g.

$SIG{__WARN__} = sub { print "warn called: @_\n" };
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-Matt