Startup Scripts run in the context of System, not the user.

This means you have about 3 options...
1. RunasInteractive User - http://www.kixtart.org/forums/ubbthreads.php?ubb=showflat&Number=198514#Post198514
2. Combination of Startup Script and Logon Script - Put System Items in one script, and user items( Drives, Printers) in another. The logon script option is per user and not a gpo.
3. RegHack - Not going to link to this because it is not supported by MS, and reduces security, however this is a "Easy" registry fix

If you go with Option 1, please leave a comment in that thread on how you used it, how it worked, etc. It has been pretty well tested but comments never hurt.