I found that the central wingate config was pretty useless at excluding EXE's (please don't be offended we have used wingate loads and its been invaluable) however with so much traffic and inconsistencies it was found easier to put the EXE name to be excluded in to the registry entries for the excluded system apps.
This stops the exe from being intercepted by WGIC and allows things to run a lot easier. I have also successfully pushed these settings via group policy to over 600 computers. If anyone wants instructions on how I achieved a much less painful wgic / wrp setup then reply and I will write it all up.
Basically its a GPO with PolicyMaker Registry Client and the Wingate registry entry for system apps with WGIC disabled for system apps.
Works lovely
Graeme