I'm running AHCI on my setup. I was tempted to change over to the IDE emulation just because the extra 15 seconds at boot pisses me off; but I have read that these WD Velociraptors will perform better with AHCI so I stuck with it.
I was having issues with my external WD ESATA drive randomly powering down and needing a restart to be detected again, but taking it off the JMicron port and using one of the Intel ports seems to have fixed that problem.
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