This is something we looked at for a while when starting out, and even posted on HN to ask about (http://news.ycombinator.com/item?id=203864). In the end, we chose Flex because it seemed like we could get good enough performance while enjoying the benefits of quicker development. We mostly use pure AS3, but we saved some time with a few components. Hopefully someday we can strip those out and cut the Flex framework overhead.
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).
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).