The problem is flashplayer identifies your full screen as both monitors, and then scales it down to only one monitor so the video looks longer but smaller.
This drove me mad for months until I found this workaround found here:
Is basically a little script than "lies" to the browser modifying the environmental variables to make firefox think your fullscreen resolution is 1024x768 and not 2048x768 in my case (you can configure other resolutions) and use only one of both monitors. You need to install nspluginwrapper first (is in the repos).
Inside the .tar.gz you'll find the script and instructions to configure it. Also, instead of calling firefox with the parameters every time, you can make a little script like this I use and save it in your personal scripts directory (for instance $HOME/.scripts/firefox
LD_PRELOAD=/usr/lib/nspluginwrapper/i386/linux/libfullscreenhack.so /usr/bin/firefox "$@"
If you want to use the same with another browser like chrome or chromium you'll only need to do a similar script for them.