I think the problem is just that Chad and Vinny are too different types of QB's, and Hackett isn't willing to adjust his offense to fit one when the other's out. Hackett's offense works perfectly with Chad, who isn't a particularly strongarmed QB, but a very accurate and very smart one.

The truly great coaches won't make their team adjust to their style of play, they'll adjust their style of play to accentuate their team's strengths.