Hmm. Well, there have been a couple of previous threads (from May or earlier) that had complaints about #3 or #5 pitchers consistently being skipped in the rotation. I'd suggest you do a search for them, but I never have much luck with the search function. They're almost certainly in Closed Issues.
Edit: Okay, here's one of them (found by manual search)
http://www.ootpdevelopments.com/boar...d.php?t=145316