This problem has been reported in several places (e.g., here and here), but the Verizon thread has been closed to new comments, so I'm starting a new thread with this post.
I have a FiOS Motorola STB connected to my Series 2 Tivo via the serial cable. About 10-20% of the time, when the TiVo changes channels on the STB, it goes to the right channel and then the STB jumps one channel - causing TiVo to record the wrong program. Other times, when changing channels via the TiVo remote, the STB will go crazy, changing to all kinds of random channels. This goes on for several seconds, like the TiVo and STB are fighting over which channel to change to. Ultimately one of them gives up and it ends up on the wrong channel. This happens most often if I try to change channels quickly (e.g., hit the channel up button several times).
Related to this problem, if the STB changes to a channel that we don't subscribe to, a Verizon screensaver will eventually be displayed. We recebtly came home from a weekend away only to find that our TiVo had recorded hours and hours of the Verizon screensaver!
Needless to say, this is VERY frustrating for us. This same setup worked flawlessly with Comcast, who uses the same Motorola box here in New England. We love TiVo and need it to work, to the point where we're considering switching back to Comcast if we can't get this working reliably with FiOS.
I've thought about getting a new TiVo and using the cable card, but then you can't use things like on-demand and pay-per-view. I'm also going to try switching to the IR blaster rather than the serial cable, but that seems like a real hack to me.
If anyone has found a solution that works, please reply.