Just upgraded to X3 over the holidays - of course, just before the new versions were announced, go figure.  Anyway, I have a Korg NanoPad2 which isn't always plugged in.  In Sonar X2, if I plugged it in (via USB) then X2 would prompt me with a "Activate this MIDI device? If you do, then transport will have to stop" or something like that.  I always clicked yes, and the nanoPad would be active and I could use it right away.
 
In X3, nothing happens when I plug the nanoPad in.  It lights up, but nothing happens in X3.  If I close the program and restart it, the device is available.
 
What gives here?  I shouldn't have to close and open just to use my nanoPad.
 
Thanks for any help here.

I have the same problem with Novation Launchkey. Computer detects it connected but Sonar some time sees it when I open it or restart program and some time it does not. I actually have to unplug it and plug it back and then it detects it. I thought I was the only one having issue. I contacted Novation- they sent me replacement cable. Have you tried different USB port? I would say- make sure your device is connected and power ON before you start Sonar. Also in my case it does not help. But it always sees Yamaha USB, so go figure.