I have two of those Frontman guitars as well (the yellow versions that the remotes slip into), and I was also having those problems last night. At first, neither of the two guitars would connect. After a few tries, one would connect but not the second. Still don't know why that was / is, but eventually I got them both to work. What I do is boot the game and then keep resetting until it works.
It's like the remote doesn't remap to the guitar buttons or something. If you notice when it doesn't let you navigate the menus with your guitar only the + button on the remote itself will work while plugged into the guitar body. But I do find that the reset button eventually gets it working. You can tell the guitar is working correctly when it allows you to skip the safety screen with the green fret button.
But I agree. This guitar was compatible with everything and now this game goes and messes it up (or at least makes it much more frustratingly difficult). If you figure out a better solution, please send it my way or post it here on the forums.