@darkconz , I'm more new at this SAS stuff than a lot of folks here, so allow me to "fill in" some detail that was new to me and so may not be known to you:
Normally, your HBA/RAID Card (the LSI SAS 9300) connects to the backplane with SAS cables that include the extra wires for sideband signals. The sideband wires control the LEDs on the front. These wires are separate from the wires that carry the data to the drives. Generally, the backplane would be expecting jumper j84 to be set to SGPIO, as its the default set-up for sideband signals in the "A" or "T" or maybe also "TQ" backplanes via the cables. For those backplanes, the sideband wires have to be present for the LEDs to function correctly.
Even from Supermicro, Broadcom, etc. some SAS cables are intentionally manufactured to not have sideband wires (which makes them cheaper to make, easier to bend, etc.) for situations where they aren't necessary. Some generic cables lack the sideband wires simply because its cheaper to make. Supermicro and a few others use a different color/style wire for the sideband. I assume its because its a different gauge or something. I don't think they need to be as robust as the wires carrying data. For generic cables...who knows.
A last long-shot thing to check is the power connectors. Even if you are only putting a couple drives in the system, you have to have ALL the power connectors on the backplane plugged in. Your's has 6? Normally, a missing power connection would also give you an alarm, not just odd behavior. But if it came to you with the alarm jumper on silent....
Cheers!