It did this to me when I brought it home on release day to my softmodded Wii. Are you using Preloader to block updates from the disc channel? I was, and I kept getting the behavior you described until I changed the setting in Preloader to allow updates, started the game and -- stupidly at the time not knowing if it was safe or not, but I wasn't waiting to play that -- accepted the update it asked to apply. After that the game worked fine.
It didn't seem to harm my homebrew setup in any way; it didn't update my System Menu (whatever version it was back then, can't recall), delete the HBC or anything like that, and it didn't interfere with the RawkSD for Rock Band 2, which uses IOS 37, at all. I'm guessing it just installed an IOS used for TB:RB and didn't touch anything else. I'm not making any guarantees that it's safe for you, I'm not really an expert but that was my experience. I'm sure someone here is knowledgeable about all these details and can tell you exactly.
If such a person does show up, I'm very curious about the same issue with regard to RB3 being released tomorrow -- I'm guessing nobody knows before release but I wonder if it will require an update, and if so will it be a possibly safe one like TB:RB or will you need to manually update some things to run it without accepting the update from the disk?