I seem to be having the same problem.
Input 1: Foxtel dig sat
Input 2: Canberra dig FTA
The daily calls succeed but after indexing I only get the FTA lineup. I am set to download the NS12601 lineup.
I manually uploaded (suing dbload) the NS02015 lineup (the one I was using before I got the 2nd input installed) and that has worked. Is there any way I can force the tivo to download other lineups? If not I will try to redo the GS with the NSW postcode.