All of a sudden Sonar locked up in the middle of playback - well it kept playing but was unresponsive. So was Task Manager. What in the world? After taking my high blood pressure medication and ending my tirade of words I can't say in front of my grand-children, I tracked it down to, wait for it ..... 
 
       An evil Java update pop-up.
 
Yep, I confirmed that was the issue. Of course I disabled Java updates in Control Panel --> Start Up right away. Problem solved. I only installed Java because a utility required it. Kidding aside, maybe this will help someone.

Are you saying that the popup stole focus from Sonar rendering it unresponsive without painting on top of it so that you would know it was there? Or are you saying there is something poisonous about the popup itself?

No, I'm not saying there was any viral activity. Like I said "kidding aside" - this is a tongue-in-cheek post. The likely culprit isn't the pop-up but the background process that checks for updates or that connects with Oracle. Something to do with the Java updater caused the problem. I was able to repeat it several times and eliminate the issue by disabling the Java updater service. I suspect that the thread was running with a high priority and somehow interrupted audio processing - I did hear a "stutter" right before things went haywire.
 
In any event, the moral of the story is know what background processes are running and eliminate anything unnecessary. 

Haha - for my money you were right the first time Dranck:) Thankfully it would seem its days in the sun (no pun intended) on our desktops at least are numbered.

Just as a warning, if you're not willing to update Java, then you should probably uninstall it entirely. Otherwise you're just setting yourself up for security problems and potential viruses later. The auto updater process is annoying but the alternative can be worse.