Same problem here, full screen flash is choppy when watching online streams.

Tried the /etc/adobe/mms.cfg trick and the unchecking of hardware acceleration in the settings.

Setup:

Zotac Mag HD ND01 - nvidia ion 330
Ubuntu 10.04 64bit minimal install with Openbox WM
Flash: flashplayer_square_p1_64bit_linux_091510 (tried different ones)
Browsers: Firefox and Chrome