I'm in the midst of setting up a brand new SQL Server 2008 system on Windows Server 2008. I've found that configuring the separate disk drives, one for data files and one for transaction logs, it's best to use the basic disk initialized as a GUID Partition Type, or GPT, (http://www.microsoft.com/sqlserver/2008/en/us/wp-run-sql-2008-on-windows-server-2008.aspx) with an allocation of 64k (http://technet.microsoft.com/en-us/library/cc966412.aspx) when formatted as NTFS.
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