Intransitive Cartesian decompositions preserved by innately transitive permutation groups

We study Cartesian decompositions of sets that are acted upon intransitively by innately transitive permutation groups. We prove that such groups have at most three orbits on such a decomposition. A consequence of this result is that if $G$ is an innately transitive subgroup of a wreath product in product action then the natural projection of $G$ into the top group has at most 2 orbits.