It sounds like you have your TiVo connected directly to the TV with audio being passed through to the Yamaha. If that's the case, you could connect the TV to the Yamaha instead and pass the video through to the TV. The TV would be bypassed in the audio chain, so the TiVo remote should control the Yamaha volume and mute. That's how mine is set up.Exactly, that's way too long to wait and user unfriendly. The TiVo remote is programmed to control the Yamaha's volume and mute functions. I'm guessing that without Anynet+ turned on, the Samsung TV does not pass the command on to the Yamaha.
Edit: I see above that you say the signal is less soft when connected directly to the Samsung. If that's the case, I guess it's a trade off for you.