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Reboot causes Rebuild

Reboot causes Rebuild

(OP)
I have a 9240-8i card, with firmware flashed to function as a 9211-8i card in IR mode(using standard well-documented procedures). OS is Win 8.1 64-bit.
I had two 3 TB WD RAID disks configured as RAID-1 array, all was behaving well for a long time.

One disk then developed hardware issues, and was replaced by vendor (WD) with a brand new disk (same model).
Now after the array was rebuilt successfully from scratch, after ANY reboot (cold or warm) the LSI MSM ALWAYS indicates that the array is degraded, and a rebuild is happening (an 'expanding capacity' task is also present, in addition to the 'rebuilding' task).

Now here's the interesting bit. I thought perhaps the new disk somehow clashed with the original disk kept in the array (slightly different firmware, 1K02 instead of 1K01), causing degradation, so I used two entirely different WD 3 TB disks (1K01 firmware) and started from scratch again.
Lo and behold, the same thing happens. I have rebuilt the array from scratch after a diskpart 'clean' on both disks, also it makes no difference if I use the MSM or the BIOS-controlled utility. The RAID-1 array initialises correctly, also I have done a full format under the OS.
All disks are GPT, not MBR needless to say.

I have gone through this exercise a few times now and it is driving me crazy. The capacities of the 2 disks in the array are exactly the same according to MSM (and according to Disk Manager).
Could anyone please shed some light on this issue ? Nothing has really changed from my initial setup, where everything was working fine, except that 2 different disks are being used.

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