One more thing to keep in mind, you may have statistics on columns that are not in indexes. Make sure those are being updated. Your plan could potentially skip these statistics.

I agree with Igor's post. Here's some info on the trace flag: http://blogs.msdn.com/b/saponsqlserver/archive/2011/09/07/changes-to-automatic-update-statistics-in-sql-server-traceflag-2371.aspx