Thanks for the replies.
I am on Windows 7 Pro x64 with a DAW and SONAR install I have been running for about a year. As the original posters pointed out it doesn't happen all the time, but when it does the other windows simply will not stack on top of SONAR. I have to minimize SONAR to see the other windows. This includes both free standing apps such a MS Paint (when I am grabbing a screen shot) as well as dialog boxes that open within SONAR (Cakewalk Plug In Manager) but end up displayed underneath.
Clicking on the icons in the taskbar does not help... I can see the window pop open but then it disappears underneath.
If I close SONAR and relaunch it then it is usually OK again. I just did a bunch of updates to Native Instruments, Studio One 2, and some third party effects, but otherwise I can't figure out what might have changed.
I did notice that a function I thought I turned off seems to have come back to life: If I drag a app window up near the top of my display screen it auto snaps it to maximized. I can't remember how/where I turned that off before.
I'll try the suggestions made by Geoff the next time it happens.