Could be a lot of things but I suspect virus scan on the server might be to blame. Could be scanning the incoming files and slowing the whole thing down. Could also be automatic transitions that are creating new version by setting variables, that'll slow things down as well.
Where is your archive server located in relationship to the users? I am assuming it is a local server, but it if is offsite there could be a lot of unknowns. If it is onsite have you tried different connections or connecting to the switch the server is plugged into?