A system is data-independent with respect to a data type $X$ iff the operations it can perform on values of type $X$ are restricted to just equality testing. The system may also store, input and output values of type $X$. We study model checking of systems which are data-independent with respect to two distinct type variables $X$ and $Y$, and may in addition use arrays with indices from $X$ and values from $Y$. Our main interest is the following parameterised model-checking problem: whether a given program satisfies a given temporal-logic formula for all non-empty finite instances of $X$ and $Y$. Initially, we consider instead the abstraction where $X$ and $Y$ are infinite and where partial functions with finite domains are used to model arrays. Using a translation to data-independent systems without arrays, we show that the $\mu$-calculus model-checking problem is decidable for these systems. From this result, we can deduce properties of all systems with finite instances of $X$ and $Y$. We show that there is a procedure for the above parameterised model-checking problem of the universal fragment of the $\mu$-calculus, such that it always terminates but may give false negatives. We also deduce that the parameterised model-checking problem of the universal disjunction-free fragment of the $\mu$-calculus is decidable. Practical motivations for model checking data-independent systems with arrays include verification of memory and cache systems, where $X$ is the type of memory addresses, and $Y$ the type of storable values. As an example we verify a fault-tolerant memory interface over a set of unreliable memories.