because I am useing Cobra at work I have installed a copy here at home, too.
As an example when I switch to Cobra is in WavePurity. WavePurity is a software for recording and restauring i. e. old records.
When I start the Recording assistent in WavePurity it opens a window within WavePurity. NVDA show the items, buttons etc. in this windows - until I switch to another running programe like Mail, Internet, Text etc. (Alt+Tab).
When I switch back to WavePurity, NVDA only shows the main window. I have no idea how to reach the Recording Assistent window again.
In Cobra I hear an acoustic signal that there is another available window. With Cobra-key+a I can switch to this window inside of WavePurity.
May be it only is my lack of knowledge of NVDA that I can do the same wihtin NVDA, but because I know how it works with Cobra I use Cobra when I work with WavePurity.