Same number of files, are they on their own spindles, same type of raid able to handle the same iops. Is you disk alignment the same on all drives on both machines?

Do you have instant file initialization turned on, with both machines? Log and db growth rate settings the same on both machines? Is the log on it's own spindles on both machines?

Was this an existing server that only became slow after 1 change (upgrading to sql server 2008 R2)? Or were there other changes done at the same time?