I had the same problem when using Chrome. Chrome, unlike other browsers, does not use the Flash plugin installed on your system but its own embedded plugin.
The problem is that this version does not work well on Ubuntu 12.04 when using multiple screens. So you need to force Chrome to use the default system Flash installation (the one that you use in other browsers, e.g. in Firefox).
To do that:
chrome://plugins in the address bar
- Click the button "details" on the right side of the screen.
- At this point you will see two versions of the flash plugin:Disable the one that has the most recent number version.
- Reload the page where the flash content is.
That should solve the problem.
Please note that you will still have the issue (which is different from the one you are experiencing) that full screen videos will always start in one of your monitors, regardless of where your Chrome window is located; just follow the link below to fix that.:
How can I force fullscreen on my right screen?