Hey there,

It's the way 9x works, in the opposite way of NT. NT first loads the userprofile, then executes the policies and then starts the execution of a login script. 9x executes the script first and then loads the userprofile.

The solution is to execute a second/post script while explorer starts. The userprofile is then loaded. You can start the script in two different ways.
-Setting registry string.
(eg. WriteValue = ("HKLM\Software\Microsoft\Windows\CurrentVersion\Run", "PostScript", "C:\Windows\KiX32.exe \\ScriptServer\Share\PostScript.kix", "REG_SZ")
-Put a Shortcut or Batch File in the Start Up directory, to start the script.

In my opinion the first option is the best. Write the value for starting the second script, in the first/login script.