Hi Michael Murray,
That is an excellent question. It is unfortunate that you are having this issue. How the Slingbox controls the TiVo is using IR remote control signals. Since the Slingbox is controlling both devices, that would mean that both use the same IR signal, even with being on different remote codes.
You will need to either change the TiVo not connected to the Slingbox from IR to either RF or UHF is available. Or you will have to block the signal from reaching the TiVo that is not connected to the Slingbox.
Hope this helps,
Sling Media Moderation Team