On the Premier the remote code in Sys Info shows "1 (IR) (RF)" but it still responds to both the 1 and 2 setting on the remote! Why?
The same thing happens on the S2 which is set for the 1's code.
According to this both Tivos are set to remote code 1 and so are both switch positions on the remote.
Are you completely blocking the IR receiver on the Tivo that you are not programming at the time?
Are you navigating to the system information screen when you are setting up the remote code and then exiting that screen before using the other Tivo?
FYI - You don't have to use code 1 for position 1 and code 2 for position 2, you can use any one of the 9 remote codes for each of the dvr switch positions (but not the same one for both)