Visibility of shared desktop

My student can't see the chat or transcript boxes when I open them.  I typically have a learning website open for him and I share my desktop.  If I add a window, I can go to maps or another website and he will see those.  

However, in the lesson, when I point to the chat box or transcript, he can't see those boxes which I have on my desktop?  

I don't get it?   

Thanks for any help.  

Paul