No, I didn't do that. Once I saw the problem, I did go in, searched around a bit to see if there was something I could tweak, but didn't change anything.
Edit:
Although I didn't manually change it, I have to wonder if somehow some of these settings got changed. Could someone tell me if the defaults are different than what I have?
Belt distance per tier: 4
Belt first tier distance: 3
Pipe distance per tier: 4
Pipe first tier distance: 11