The order of shutdown on a multi-shelf SAN is important. This is especially so for situations where there are Vdisks that span the shelves in the SAN. There is apparently a timestamp (specifically on the MSA 2000 series) that the controller keeps current on each of the drives in the Vdisk set and these must match for the controller to bring the Vdisk online after a power cycle.
You should power off the main controller shelf first, then any secondary shelves so that the timestamps written by the controller will be consistent.
When powering on, power on the secondary shelves first and then the main controller shelf.