\begin{align*}
Z &= \begin{multlined}[t]
\sum_{k=0}^{N-1} \tr \bigl\{ Q^{-1} \bigl[ (P_{k+1} + x_{k+1}^N x_{k+1}^{N\prime}) - (P_{k+1,k}^N + x_{k+1}^N x_k^{N\prime}) A' \\
- A (P_{k,k+1}^N + x_k^N x_{k+1}^{N\prime}) + A(P_k^N + x_k^N x_k^{N\prime})A' \bigr] \bigr\}
\end{multlined} \\
&= \begin{multlined}[t]
\tr \bigl\{ Q^{-1} \bigl[ (P_{k+1} + x_{k+1}^N x_{k+1}^{N\prime}) - (P_{k+1,k}^N + x_{k+1}^N x_k^{N\prime}) A' \\
- A (P_{k,k+1}^N + x_k^N x_{k+1}^{N\prime}) + A(P_k^N + x_k^N x_k^{N\prime})A' \bigr] \bigr\}
\end{multlined}
\end{align*}
renders as
Obviously the vertical spacing within the second multlined environment is too cramped, and if not for the sum providing a buffer the spacing in the first one would be too cramped as well. How can I fix this?

\\[1em]for example or any other value. – Sigur Jun 01 '16 at 01:58emis a unit of horizontal space. better to use a vertical unit.\jot, as cited in an answer this question How to increase the spacing between equations in “gather”? would be a good candidate. – barbara beeton Jun 01 '16 at 12:54