I deploy Win2K and Win2K3 servers via Unattended install and follow that up with a 'guirunonce' that does my post OS install steps.

The guirunonce runs a vbscript that handles the rest of the server configs necessary. I've noticed on both 2k and 2k3 that when it boots up and logs in the first time, the script begins its business.... but the desktop doesn't really show up until the end of the script (right at the 'reboot' in the script).

Anyone know what / why I'm experiencing this?

The GuiRunOnce section adds the commands to the HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnce key, which is designed to work like that. Check out the Windows setup timeline reference for more info.