Hello,
We are observing the same issues at present. We've had the entire MSA 2040 replaced by now and the issue persists.
Have you tried the latest firmware for your HBA? I'm guessing we're using the same HBA:
HP StoreFabric SN1000Q 16GB 2-port PCIe Fibre Channel Host Bus Adapter
(QW972A)
We have not seen these issues with other MSA and HBA combinations.