Why don't you try putting your script in to the respective policies, computer startup folder e.g. (\\moo.ac.uk\SysVol\moo.ac.uk\Policies\{AAFCDC9F-8E7E-42BE-A0E5-879FB1C61811}\Machine\Scripts\Startup).
I had similar probs before like this when executing startup scripts from netlogon
Also you could try executing cscript.exe and specifiy your vbs file as the parameter
I am experimenting with using RemoteApp to fuel this pain-in-the-a55 of a product, the product appears to work fine on the terminalserver 2k8r2-nosp but only up to the login screen just need to get a few mock tests and try the remote app method on my clients.