This has been covered recently. With lower spec machines.... Flash 9 runs horribly. Nothing we can do. Adobe built us a piece of junk. Mplayer with it's own codes, works much better as you have discovered.
My old box (God rest it's good soul) was a 1 gz with 500 mb ram. I couldn't comfortably run flash 9 either. Yet using Windows on the same machine, Flash 9 worked great. I guess they didn't put enough love into our version.