Is this an onboard controller or an external? A typical external RAID controller (and some internal) have a BIOS that loads on POST which may show you whether it's active or not.
Otherwise, most BIOS post messages display the IRQ info of onboard components during boot so you should technically see a SATA/SAS/RAID controller there.

I'd suspect the drive or corrupt boot loader first.

What OS is this?

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@gjacobse https://sourceforge.net/projects/supergrub2/files/2.02s9/super_grub2_disk_2.02s9/super_grub2_disk_hybrid_2.02s9.iso/download

Considering the solution - I have been thinking for several days that perhaps this issue stemmed from a problem with the disk on the original system. It might be slightly damaged - somehow not enough to prevent it from booting, but enough to cause the seen issues in the clonezilla image.

If I cared, I could run chkdsk /r on the system a few times, then take a clonezilla image again, and then try restoring that.

meh.