Windows has more security contexts than just which user the script is run under. The CGI script likely doesn't have access to the desktop (can't open windows on the desktop) and I'm not surprised that it doesn't have access to mappings to network drives that were created from the desktop. It appears you can access the network drive (which isn't always possible from CGI scripts), so you could also just map the network drive.

It may also be the case that a drive mapped by one CGI script will be visible to other runs of CGI scripts, so you'd only have to map it once. Try it and see. Just map the drive if you find it isn't mapped.