hi guys, i accidentally stumbled upon this problem too, luckily tho, as the micro-freezes caused by the constant load/unload were really driving me insane (i run a raid 0 so i think the issue is worse as the load cycle will take more than just for 1 drive)
i was pretty disappointed to find out there isn't a fix for this problem yet, but then again, as i searched more and thought about it, i think we may never see a "fix" because this is not really a bug, rather it's the intended behaviour. It seems infact that the idle timer is set into the HDD's firmware and the controller can't do much about it, heck, i don't think it even has a way to know about it. So i guess that while it would be nice of Intel to give us an option under RST to completely disable APM, i think we may not see it at the very least for the foreseeable future.
anyway, since this was a big problem to me, and since the "solutions" (rather, workarounds) out there didn't satisfy me at all (or just flat out not worked) i went ahead and wrote a small utility that takes care of keeping that pesky APM disabled for my drives. Yes, i know there are some other utilities that do just that, but they are not compatible with Raid, or just flat out suck.
so here it is, it's a very simple and small program, it's open source and it uses smartmontools to perform the calls to S.M.A.R.T.. you can find it at this link noapm - NoAPM is a small tools that relies on smartmoontools to keep hdd's APM disabled - Google Project Hosting
if you have any questions or problems let me know, i've been using it for a few days and it runs great.