Hardware acceleration is not available in fullscreen mode for Linux yet, at least not with Adobe’s Flash 9.x plugin. This isn’t much of a problem with small videos, but it results in choppy, sluggish playback in fullscreen mode. Fortunately, there’s a simple way around this while we wait for Adobe to address the issue.
If you’re using compiz-fusion, a simple fix is to enable Zoom Desktop in the CompizConfig Settings Manager (command “ccsm” or System->Preferences->Advanced Desktop Effects Settings in Gnome/Ubuntu).
Now just zoom into the small video. You need to play around with the settings a little to make it easier to get the video centered (decrease zoom step, etc). It works perfectly.
This is actually a nice hack. It’s simple and gives you the option of zooming in further than fullscreen takes you, and you can choose certain parts of the video. Yes, you would be able to do this normally by resizing and moving the window if HW acceleration was available, but I like being able to quickly zoom in and out with the mousewheel.