Exact same problem:
4xWD3200KS drives gone using staggered spinup on the Highpoint 2320.
The disks work as long as they are connected to the 2320 controller
and using the controller drivers in XP. But FreeNAS doesn't recognize
them anymore.

I can make them spin up on my mainboards controller using the linux
disk, but it fails to disable the feature.

I have filed a question with WD support, hoping they can help me. I
think it should be solvable by software or maybe a firmware reset/
update of some kind.