I'm using my Roland A-800PRO MIDI controller through a soft-synth single track to practice and play around a bit. Strange behavior happens when I minimize SONAR X3 and do some other unrelated tasks on the computer for a while. (These are usually Firefox related tasks, with no sound being played). Sometimes the keyboard drops out - no sound when I press a key. If I have some notes recorded in the track - when I play the notes they start to play after a slight delay. Then, usually, the keyboard works again, but sometimes a SONAR reboot is needed. It's like it goes to sleep.
 
MIDI controller is hooked up with the OEM USB cable plugged directly into the computer (as suggested in the manual), power supply turned on (same happens when USB powered).  

Try un-checking Share Drivers with Other Programs under Preferences > Audio > Playback and Recording.
 
 

Under Preferences > Midi >Playback and recording
I have to uncheck System Exclusive and Patch Changes and Controller depending on the midi input I use. Some synths can't handle some of these midi messages and the synths kinda freeze. Dim Pro and Rapture do this to me. Not so much with Zeta.
 
For me, this is most likely to occur when I hit the patch change stomp on my Roland GR20. That message tends to mess up some synths. Others just change patch too (not usually what I want :-))

I unchecked Share Drivers with Other Programs and now it seems to be OK. I have left it up several hours and done some browsing, etc and the MIDI keyboard is still active. I remember checking the Share Drivers... option some time ago in order to be able to watch a Youtube tutorial and try it out on Sonar - going back and forth quite a bit. I couldn't hear Youtube once Sonar was up or vice versa. Checking the option fixed this. However, NOW when I uncheck the Share... option, I can hear Youtube and Sonar simultaneously. Seems like I shouldn't be able to hear Youtube and Sonar at the same time with Share... unchecked (I couldn't before). I don't quite understand this part. But, it's working the way I need it to now. Thanks!
 
Meanwhile, I learned to use the Stop Audio Engine and Reset Audio buttons (in the transport panel), which would let me switch between Sonar and Youtube also.

jdwroten,
 
I think if you have two apps that have different specified sample rates then you can get into trouble switching between apps. It's best to use the same sample rate. Like if you're project is at 44.1 and you want to record a screen capture video, pick 44.1 for the audio of the screen capture and your thing will come out better.

Share drivers with other programs is a little poorly named.

What happens is that while it allows an audio device to be shared with other programs the program that has the driver is the one with windows focus. So the sharing is on an exclusive basis.

Leaving this unchecked allows all programs to access the driver simultaneously but only if they share the same sample rate. Audio and MIDI drivers are linked in many behind the scenes windows activities so this explains why your MIDI connection to sonar was lost when it was minimised.