I've just replaced my old Lexicon Alpha with a lovely new Focusrite Scarlett 2i4 (2nd generation). As soon as I connect it up, the standalone versions of Rapture Pro, Rapture Session and Z3TA+2 stop working. Disconnect and reconnect the Alpha and all's well. It works OK within Sonar although latency is just the same as with the old Alpha with it's old Windows 7 drivers.
Has anyone else had a problem with Focusrite drivers? I've got a show in 3 weeks time and need everything working before then, so it's either get this working or go back to the old Alpha interface and look for a refund on the Scarlett.
 
Also should mention that EZdrummer 2 and Real Guitar are also giving me a problem, while SampleTank 3, Addictive Drums 2 and BFD3 are all working great!

Do you still have Alpha connected when you start problematic programs? If not, connect it simultaneously with Focusrite, start the program and switch its output from Alpha to 2i4. After that these programs should work with Alpha disconnected.
 
Note that ASIO buffer settings (software latency) are separate for each device. Defaults are rather conservative.

Not only have I disconnected the Alpha but uninstalled the driver. Starting up the instruments with the Scarlett disconnected - I get a warning about no sound card. Connected up they just crash before starting.

Did you follow the instructions carefully as you installed the latest driver from the web site? 
You have to wait until asked to plug it in, Always use the same USB port too. 
And does it show in Sonars audio preferences that the Scarlett is in ASIO mode and is the timing master? 
 
 

If it helps, when I experimented with a Focusrite beta driver, Focusrite Support was excellent helping me fix my clicks and pops by rolling back to the stock driver.  However, it wasn't just a case of uninstalling the driver.  I had to follow Support's many-step process to delete the old driver fully.  I recommend you get advice from Support.
 

Contacted Focusrite support - just waiting for a reply. Strange some standalones work while others don't. Tried it with VSTHOST and SAVIHost yesterday with no issues, so it seems that all the VSTs work fine and the issue is with how the standalones call the ASIO driver.

Did the Alpha use ASIO drivers?  

The Alpha used ASIO drivers but there were none for Windows 10 and they advised me that it was not a high priority to get them done.

Focusrite have just sent me their latest driver and it works a treat. Everything is now working and Sonar is even using less CPU than it did before.

Good stuff. One thing I must say is they do have good customer support. I had driver issues when I first got the 6i6 and they did the same for me, which was a link to a beta driver. They seem to have buggy first issue drivers but sort them out pretty quickly.