I believe this may just be the case that the vss command line is very slow. We’ve had other users report the same issue before, and they see the same slowness when running vss from a batch file as they do with finalbuilder.
I know this doesn’t solve your problem, but if at all possible I’d highly recommend moving to a more modern version control system (such as mercurial or git). We use mercurial here for new work and I’m more and more impressed with it every day, and performance is excellent (even over my slow vpn connection from home).
Discovered issue was caused by IT moving our VSS DB to a 2008 R2 server. This did not cause any problems if the vss client was run from a physical pc. It did however, cause a major decrease in performance if the vss client was run from a virtual machine.
No idea why this is the case but we are moving the VSS DB back to 2003 Server so all is well.