You have to set the sample rate in the Scarlett software to whatever you want your session to be, BEFORE you open Pro Tools. Unfortunately there's no workaround for this, it's just the way Tools works with 3rd Party interfaces.
I'm not sure what the Scarlett equivalent is, but I use a Saffire 56 and have to set the sample rate of the device in Saffire Mix Control BEFORE opening a session. It's still a little buggy at times but FS are working on that as best they can.
Oh and BTW, make sure you have the VERY LATEST drivers from Focusrite's website as well. Don't use the drivers on the CD It comes with, they are 9 times out of 10 completely out of date.
Focusrite also has a Beta website where you can get the latest beta drivers and see if you have any luck. The 'Asio Device Has Changed Properties' error used to be very frequent with Saffire interfaces until Mix Control Beta 3.
www.focusrite.com <public drivers
beta.focusrite.com <beta drivers
Hope this helps you get started!