Read an
excellent write up on why logon scripts might stall under Vista. It is due to a design decision that I don't necessarily agree with.
The most important nugget of information from the post is below:
It is possible to disable boxing for programs initiated from the Startup folder or the Run key in the Registry.
To accomplish this, the following registry key must be changed:
Key:
HKLM\Software\Microsoft\Windows\CurrentVersion\Explorer\Advanced\DelayedApps
Value: Delay_Sec = 0 (default value = 60)
Changing the value is a bit hard because the key is owned by TrustedInstaller and Administrators only have Read access to the key. To overcome this hurdle you must first take ownership of the key.
Unfortunately programs initiated from logon scripts defined in Group Policy are not affected by this key.
Make sure not to blindly cut and paste that into your registry - please read the article above that explains it all.