I am having a similar problem however this is with just an internal sound card. I have a samsung all in one with a realtek hd audio. I just installed the realtek drivers and issue still remains. 
 
Symptoms are:

When running sonar, if I go to you tube or any other app that requires sound the sound is silent. If I open youtube first then sonar, youtube sound works but sonar is silent. I do realize this may be more of an OS/Driver problem than sonar but figures I would start somewhere.