The eigen-decomposition of positive semi-definite matrices always exists. Given such a matrix $\mathbf{A}$, then, we have
$$\mathbf{Av}=\lambda\mathbf{v}$$
for a given eigen value $\lambda$ and associated eigenvector $\mathbf{v}$, which can then be rearranged as
$$\mathbf{A}-\lambda\mathbf{I}=0$$
Here is where I get confused. It is quite possible that the off-diagonal terms of an arbitrary positive semi-definite matrix $\mathbf{A}$ are not zero, but this last equation implies that they must always be zero. What am I misunderstanding here?
That rearrangement is incorrect. The difference $A−λI$ is not 0; it is only 0 when acting on $v$.
There is, in general, no way to "divide" out $v$ from the both sides of the equation - $v$ is a vector, not a number, and generally does not have a multiplicative inverse.