I was just looking at the Saffire manual for stand alone operation. In it you can save the settings from the Mix Control to hardware. I wonder if that would help you in this. My thinking is that the hardware is set to default and by saving the preferred sample rate to the hardware it will boot up with that and not revert back to 44.1.
 
http://d3se566zfvnmhf.clo...ostandalone4.pdf 

John that's an idea -thanks will try it....!

Alex, the latest version of mix control is 3.4. Do you have the latest versin. Not sure it will solve your problem but worth a shot.
 
 http://us.focusrite.com/downloads?product=Saffire+PRO+24
 

I just did a quick test of this to verify what I was thinking. I first bring the Saffire online without SONAR open. At that point, sample rate can be changed. When SONAR is open, the Saffire allows SONAR to take control of sample rate, so even setting the Saffire to 48 and opening a 44.1 project in SONAR will make the Saffire immediately switch to 44.1.
 
To effectively create a project with a different sampling rate, all that is required is the "Default Settings for New Projects" under Preferences->Audio->Driver Settings. When SONAR is open, SONAR controls the Saffire sample rate based on the project.
 
Other things you mentioned:
- I run SONAR as administrator
- Share drivers with other programs is unchecked
- In Windows Control Panel, both exclusive modes in the Saffire Properties are checked, and it is NOT the default Windows device (specifically this is assigned to my onboard audio).

Apart from admin I have exactly the same settings Mettelus. It will still do this 'flip' thing when everything is set at 48... #1. Cheers...

John a did a full reset of the Saffire, set everything manually from the beginning and saved settings to hardware. Will see how it goes... Thanks..

John that was it. Save to hardware, then I needed to restart the interface/reboot. A full reset didn't do any harm either... Thankyou I would have never had thought!

That is cool that it works.