http://blog.killtheradio.net/technology/slow-flash-in-ubuntu/

sudo mkdir /etc/adobe
sudo echo "OverrideGPUValidation=1" >> /etc/adobe/mms.cfg
sudo echo "EnableLinuxHWVideoDecode=1" >> /etc/adobe/mms.cfg
sudo echo "WindowlessDisable=true" >> /etc/adobe/mms.cfg
sudo echo "DisableMulticoreRenderer=true" >> /etc/adobe/mms.cfg

In order for the above trick to work, you must RE-enable hardware acceleration in flash: right click on any flash video, go to “Settings” and check “Enable Hardware Acceleration.”