Can't change Flash settings from Chrome neither Firefox
Solution 1:
This is known problem which happens when you are using composite manager (Unity 3D, Gnome with Compiz…) and the site with embedded Flash has scrollbars.
To make Settings window responsive, you need to use fullscreen. For example go to YouTube video, switch it to fullscreen and then open the Settings (it may take two or more attempts before the window actually opens).
Solution 2:
This problem has been around for a while and it affects me too. Luckily, however, there is another way to edit Flash settings here.