I found what I was thinking of - it's not the newer firmware, but just some tests that were done to show that Input 1: Guitar/Input 2: Same is not the worst way to go.
Here's one discussion - by the end there was a comment to this effect:
Later these two had a much more thorough discussion:
Not meaning to start a war or anything. I just remember using it a couple of years ago and following the initial recommendations (not using Input 2:same) and feeling like stuff didn't sound right. Then I saw the later posts and switched to Same. I had to rebuild patches, but it didn't take me that long and I felt that stuff sounded better. For the record, I am not using low output pickups - my main axe is a Flying V with a 500 in the bridge.