This happened to me after reverting from the now discontinued Flash 64 bit alpha to running 32 bit Flash via nspluginwrapper. Flash videos would load and play normally, however none of the controls were responsive, and all clicking on them actually did was the focus the window. This meant that if you clicked on a window and held down, you'd then be able to use any keyboard hotkeys to control the video. Incredibly irritating!
A triage solution appears to go along the lines of:
sudo gedit /usr/lib/nspluginwrapper/i386/linux/npviewerAdd the following just before the last line of the file:
export GDK_NATIVE_WINDOWS=1Restart the application. In my case this only affected Firefox, whereas Chromium and Opera both still functioned normally without this fix.
In any case, hope that helps - when Flash plays up it can be a bit of a show-stopper.