I then looked if there was a new Firmware for my 9300-16i and funnily there was, but also I noticed that I hadnt flashed BOTH sides of the controller.
Num Ctlr FW Ver NVDATA x86-BIOS PCI Addr
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0 SAS3008(C0) 16.00.10.00 0e.01.00.03 08.37.00.00 00:19:00:00
1 SAS3008(C0) 05.00.00.00 05.00.00.01 08.11.00.00 00:1b:00:00
So I flashed them both this time to the latest 16.00.12.00 & BIOS.
Restarted and testing seems good now.
SavellM's post in A Few drives will not spin down was marked as the answer