The geodesic deviation equation can be written in the following form $$ \nabla_U^2 \xi = R (U, \xi) U \tag{1} $$ where $R$ is the Ricci tensor. It can also be written component-wise using the Riemann tensor $$ (\nabla_U^2 \xi)^\alpha = R^\alpha_{\;\, \beta \mu \nu} \: U^\beta U^\mu \xi^\nu \tag{2} $$
I'm interested in this equation on a Riemannian manifold equipped with the following metric tensor $$ g = -(1+2\phi(x))\mathrm{d} t \otimes \mathrm{d} t + (1-2\phi (x))\left(\mathrm{d} x \otimes \mathrm{d} x + \mathrm{d} y \otimes \mathrm{d} y + \mathrm{d} z \otimes \mathrm{d} z \right) \tag{3} $$ with the standard torsion-free and metric-preserving connection $\nabla$. I'm only interested in the spatial part of the Jacobi equation, that starts from $U = e_0$ i.e. $$ (\nabla_t^2 \xi)^i = R^i_{\;\, 0 0 \nu} \,\xi^\nu \tag{4} $$
In textbooks it can be found that in the weak-field limit (keeping only the linear terms involving $\phi (x)$) this reduces to $$ \frac{\mathrm{d}^2 \xi^i}{\mathrm{d} t^2} = - \phi_{,ij} \, \xi^j \tag{5} $$ where comma indicates partial derivatives.
However, when I try this for $g$ above, I get a different result. First, the left-hand side of (4) is $$ \nabla_t \xi = \left( \xi^\mu_{,t} + \Gamma^\mu_{\;\; \nu t} \, \xi^\nu \right) e_\mu $$ $$ \nabla^2_t \xi = \left( \xi^\mu_{,t} + \Gamma^\mu_{\;\; \nu t} \, \xi^\nu \right)_{,t} e_\mu + \left( \xi^\mu_{,t} + \Gamma^\mu_{\;\; \nu t} \, \xi^\nu \right) \Gamma^\lambda_{\;\; \mu t} e_\lambda $$
The Christoffel symbols are in general $$ \Gamma^\alpha_{\;\; \mu \nu} = \frac{1}{2} g^{\alpha \lambda} \left( g_{\lambda \mu, \nu} + g_{\lambda \nu, \mu} - g_{\mu \nu, \lambda} \right) $$ so in our case $$ \Gamma^0_{\;\; \mu \nu} = \begin{pmatrix} \phi_{,0} & \phi_{,1} & \phi_{,2} & \phi_{,3} \\ \phi_{,1} & - \phi_{,0} & 0 & 0 \\ \phi_{,2} & 0 & - \phi_{,0} & 0 \\ \phi_{,3} & 0 & 0 & - \phi_{,0} \end{pmatrix} $$ $$ \Gamma^1_{\;\; \mu \nu} = \begin{pmatrix} \phi_{,1} & - \phi_{,0} & 0 & 0 \\ - \phi_{,0} & - \phi_{,1} & - \phi_{,2} & - \phi_{,3} \\ 0 & - \phi_{,2} & \phi_{,1} & 0 \\ 0 & - \phi_{,3} & 0 & \phi_{,1} \end{pmatrix} $$ $$ \Gamma^2_{\;\; \mu \nu} = \begin{pmatrix} \phi_{,2} & 0 & - \phi_{,0} & 0 \\ 0 & \phi_{,2} & - \phi_{,1} & 0 \\ - \phi_{,0} & - \phi_{,1} & - \phi_{,2} & - \phi_{,3} \\ 0 & 0 & - \phi_{,3} & \phi_{,2} \end{pmatrix} $$ $$ \Gamma^3_{\;\; \mu \nu} = \begin{pmatrix} \phi_{,3} & 0 & 0 & - \phi_{,0} \\ 0 & \phi_{,3} & 0 & - \phi_{,1} \\ 0 & 0 & \phi_{,3} & - \phi_{,2} \\ - \phi_{,0} & - \phi_{,1} & - \phi_{,2} & - \phi_{,3} \end{pmatrix} $$ which, for $(\nabla^2_t \xi)^i$ gives (to the linear order in $\phi$) $$ \xi^i_{\;\;, 00} + \phi_{, i0} \xi^0 - \phi_{,00} \xi^i + 2 \phi_{,i} \xi^0_{\;\;, 0} - 2 \phi_{,0} \xi^i_{\;\;,0} $$
The right-hand side needs $R^i_{\;\; 00 \mu}$. First, due to the symmetries, $R^i_{\;\;000} = 0$, so we only need $$ R^i_{\;\; 00j} = - \phi_{, ij} - \phi_{,00} \, \delta_{ij} $$
Now put it all together $$ \frac{\partial^2 \xi^i}{\partial t^2} + \phi_{, i0} \xi^0 - \phi_{,00} \xi^i + 2 \phi_{,i} \xi^0_{\;\;, 0} - 2 \phi_{,0} \xi^i_{\;\;,0} = - \phi_{,ij} \xi^j - \phi_{,00} \xi^i $$
Cancel out common terms $$ \frac{\partial^2 \xi^i}{\partial t^2} + \phi_{, i0} \xi^0 + 2 \phi_{,i} \xi^0_{\;\;, 0} - 2 \phi_{,0} \xi^i_{\;\;,0} = - \phi_{,ij} \xi^j $$
There are problems with this expression. It does not match what the textbooks say.
Even if it did, how can I get "$\frac{\mathrm{d}^2 \xi^i}{\mathrm{d} t^2}$" instead of the partial derivative? Is $\frac{\mathrm{d}}{\mathrm{d} t}$ to be interpreted as $U^\mu \partial_\mu$? In that case if $U = e_0$, we would have $\frac{\mathrm{d}}{\mathrm{d} t} = \frac{\partial}{\partial t}$, but probably only at the initial point of our geodesic...or do we reparametrize the geodesic in terms of the time $t$ and then derivative w.r.t $t$ is actually derivative w.r.t. the curve parameter, so $\nabla_U^2 = \frac{\mathrm{d}^2}{\mathrm{d} \lambda^2} = \frac{\mathrm{d}^2}{\mathrm{d} t^2}$? That would certainly interpret the left-hand side of (4), but we would still have that weird term $-\phi_{,00} \xi^i$ on the right-hand side (unless we assume that $\phi$ does not depend on time, on the top of all that). But even if we do it, then $U$ is no longer in just zeroth direction so the right-hand side will feature two $U$ terms (even if we begin with $U = e_0$, can it stay that way for the entire geodesic? or do we assume small $v$, therefore the zeroth component dominates and since $U \cdot U = -1$, then $U^0 = 1$?)
There's a bunch of other terms that don't seem to arise in textbooks, but I never saw the expression (5) derived, only stated.
Is there a conceptual mistake in my thinking, or I miscalculated something?