Originally Posted by Donbadabon
Check your Harmony code. If it is set to '0', that is the universal TiVo code, and will control any TiVo, regardless of the boxes code.
Donbadabon is right.
Here is the solution I posted a few weeks ago:
First you pair each TiVo to its own original remote, as described in the TiVo manual. Then for each TiVo device on your Harmony web page you need to do this:
Click on "More Options"
Click on "Confirm infrared commands"
Go through the IR confirmation process, using the paired TiVo remote for that device.
If it asks you to press the non-existent power button, just click "Skip" and go to the next one.
When you are done it should say "a better set of commands have been found" or something similar.
Then do the same thing for the other TiVo with its paired remote.