I haven't kept up with this, but I don't think there is any way to play PS2 GH games on the PS3 with a guitar controller. There are some adapters, but I seem to remember that they are sketchy at best.
I had this happen to me, too. My problem was that one of my controllers (and just one) would send out a random signal every 15 minutes or so. Sometimes it would bring up the menu, sometimes it would skip the movie forward, etc. I just figured out which controller it was and made sure it was...
It was a huge factor for me as I've never owned any version of Playstation and plan on playing PS1 and PS2 games that I've missed until the price drops on PS3 games. :)
I ordered from Dell a week ago (to skip the madness of trying to track these down in store) and they show a ship date of 12/11. Hopefully that will hold up, but who knows how many orders Dell has taken for these.