The reason for the minus sign is because there are two different rules for covariant derivatives, depending on whether the index is raised or lowered. I'm less comfortable with the comma and semi-colon notation, so let me use the notation I'm familiar with:
[itex]\nabla_i A^j = \partial_i A^j + \Gamma^j_{i k} A^k[/itex]
where I'm using [itex]\nabla_i X[/itex] to mean what you would write [itex]X_{; i}[/itex] and [itex]\partial_i[/itex] to mean what you would write [itex]X_{, i}[/itex]
For tensors with lowered indices, you get a minus sign:
[itex]\nabla_i A_j = \partial_i A_j - \Gamma^k_{i j} A_k[/itex]
For tensors with both kinds of indices, you get some minus signs and some plus signs:
[itex]\nabla_i A^{j}_{k} = \partial_i A^j_k + \Gamma^j_{i m} A^m_k - \Gamma^l_{i k} A^j_l[/itex]
One other thing you have to remember is that in an expression such as [itex]\Gamma^j_{ik} A^k[/itex], the repeated index, [itex]k[/itex] is a "dummy index", which means that you can just as well write it as [itex]\Gamma^j_{ip} A^p[/itex], or using any other symbol. What's important, though, is that you have to choose the "dummy" index so that it doesn't clash with any other index. So you can't choose [itex]i[/itex] or [itex]j[/itex].