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If the Server is doing anything at all, it knocks the encryption process to the background. By Default, SafeBoot sets the encryption process to low priority. Since it is low priority on a server that may be doing a lot of things, it could take days to fully encrypt. If you shut off all communication to the server and let it set there it will probably encrypt much faster.
Maybe the w2003 server has a really slow hard disk?
Did you apply the Windows 2003 SP1 updated fileset to that machine? It was an optional fileset in SafeBoot 4.2. Also, because I don't remember... are you running the latest version of 4.2? Is there a reason you haven't upgraded to 5.x? SafeBoot 5.x is 2-4 times faster at encryption than 4.x.