Hi Dennis,
do you also create DWFs on check in? If so this White Paper will help you reduce the time it takes to create the DWFs on check in and hence the overall time for checking in an assembly: http://images.autodesk.com/adsk/files/publishing_options_for_autodesk_vault_2009.pdf
Best regards,
Thomas Schwaiger
Customer Success Engineer | Data Management | Autodesk