Dos Vs Windows on Novell Network

We are running a dos program on a novell Network. Whenever we run the portion of the program that Indexes the database from a dos computer or a computer booted to dos it takes about 8 hours to run.
When the program is run from a computer that has windows and is run from a dos prompt thru windows it takes the same command about 20 minutes.

Is there a setting I am missing somewhere?