That behavior is expected - basically, when you click on RR (button, indicator or even empty space) windows sets RR into focus which causes the embedded application to go behind RR's screen.
Now that you know the "issue", there are two ways to deal with it:
1-You can clip off the application area ("A" definition) so that when you click on RR the area of the application is empty and will not cover it (preventing the app from flashing)
2-You can set the application to run "on top" - this is a more complex and more advanced approach (but may be simpler if the application itself has such option) - RR itself has a command to set the application on top if you want to use it. I have not double checked but maybe mitch's advanced options provide that directly as well - definitely worth looking at those new options.
I should have some time this week to see if I can do something about this once and for all,