Sorry, I made a mistake: I was thinking you are producing sound when the player hits a key - but you aren't. I think that's not part of the "guitar hero" concept anyway (it is in a drum version I saw in an arcade; a different story).
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. :-)
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).