Drives appear to negotiate at 3.0Gbps, which is good.
However, I wonder whethe same thing is what is causing Windows Server 2012R2 to not be able to toggle the drive lights (Failed to toggle drive light: Not Supported)
I've just been through the above steps, with a HP SAS expander card that had Firmware 1.00 installed, and it has not updated... even after a power cycle.
Rig:
Norco RPC-4224
SuperMicro X8SIL-F
IBM M1015 - Flashed to IT Mode with Avago/LSI 9211-8i firmware 20.00.07.00
Using Ubuntu 16.04.01 Live...
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