It could be a loose wire or solder join that's coming out and then remaking a connection, causing the boot sound to play. It could also be a switch issue. I think we'll rule out bad batteries, since you checked all of that and even tried another pair of Li-Ions. Is the saber still under warranty? If it is, send UltraSabers a quick e-mail explaining the issue:
[email protected]If it's under warranty, they'll advise you and probably fix it for free. I'd advise doing that, rather than taking anything apart to look at things, as messing with the electronics will void your warranty. If it's not under warranty, you might as well take it apart, at least somewhat, to look at the wires and see if anything came loose. If you have any skill at all in wiring, it may be something that's simple to fix and will only take a few minutes. If not and you'd rather leave it up to people who do this kind of thing all the time, you can still e-mail UltraSabers and they'll fix it for a fee. Though, due to Harvey and DragonCon, they may not be quite as fast to respond as usual, so be patient if you go that route.
Anyway, those are my suggestions. Good luck.