The default remote address for Tivos is "0". If you use a remote that is using this address, it will control ALL Tivos, no matter which address you programmed them to respond to. Make sure that any and all Tivo remotes you are using have been changed to different addresses, none of which is the "0" address.
You then have to program these distinct codes separately onto your Pronto.
It can get to be a real PITA, especially if you accidentally "reprogram" your Tivo addresses.
One other thing to keep in mind: When you are in your Tivo program menu where it shows your remote address, if you use another remote with a different address, that Tivo's address will be changed. For example; you are in the program menu of Tivo 1 which you have previously set as address 1. You inadvertently use the remote for Tivo 2 which has been set to address 2. Tivo 1 will now have a remote address 2 and will no longer respond to a remote programmed as address 1.
I hope this is understandable. The first time this happened to me, I was scratching my head for hours trying to figure out why one of my Tivos wasn't working.