For those not keeping up... The last issue I have with Vista was detailed here.
The basic problem was that administrator programs were not recognising clicks events when they were not the foreground application.
The today I noticed, completely by accident, that My VS (a "Run as Administrator" application) DID recognise a "right click".
That set me thinking about click messages and interception and that's when it hit me..... I run a third party App (Nifty Windows) for it's ability to toggle the StayOnTop bit of any window I choose. It does this by intercepting the Win+LClick key/Mouse event.
The problem seems to be that "Nifty Windows" intercepts the left click but is apparently (I'm guessing due to Vista security practices) is unable to send those clicks to any program which is elevated.
The solution: run Nifty Windows Elevated
Oh the relief :D