However, it now seems the eeePC is the main factor, as it's straining at some other points in the UI.
But for right now, music games on Flash can't live up to the expectations set by games on other platforms.
But not in terms of design: for although a Java version theoretically could be as pretty as your Flash version (and it is very pretty), the designer-tool support really isn't there. It would be hard to port; and hard to modify. Sun has some tool support for designers, but I'm sure it has nightmare usability.
I think both design and responsiveness are crucial in your space, so this is a difficult one.
But yes, Flash player has an unpredictably crappy internal clock and performance varies significantly based on the browser and OS, so synchronizing the notes with the music has been a challenge. For the most part, I think we've done a fairly good job compared to the existing players. We scale intense tasks dynamically in game but there is definitely room to improve (custom a/v delay, controller delay, really-crappy-performance mode, etc).
Anyway, I found that java can play user-triggered sounds instantly (or perceived as such), whereas Flash can't. I experimented with this in Flash, researched it/asked about it on FlashKit - and all the Flash music games I found with triggered sounds suffered from this same problem. So it's very likely true, but not relevant for you. :-)