(Yes, I know this is a late followup)
When running in Passthrough (JBOD) mode the card is unstable and tends to lockup after a few days/weeks (either 1 port or the entire card). This is a known problem with LSI SAS2008 controllers when they are in IR (RAID) mode.
It is possible to flash the device using LSI SAS9240-8i IT firmware but that means jumping through quite a few hoops.
It'd be nice if there was a genuine intel IT flash for the card. Is there any chance you can provide one?
Where do you see that this is a known problem with LSI SAS2008 controllers when in IR (RAID) mode?
If the card is unstable and tends to lockup after a few days/weeks, I do suggest updating the firmware and driver to see if that resolves the issue.
I do not recommend updating with LSI firmware.
This has been an item of discussion on various ZFS and NAS lists for a couple of years. Search for "SAS2008 IT firmware" and you'll get the idea.
I'm already running the latest firmware version (flashed it from this site about 2 weeks ago) and I'm still having trouble.
Power supplies are clean and memory is ECC. I've eliminated everything except the card and the next step is a LSI flash or changing it out.
As far as drivers go: I'm using Linux 3.11.0, which is pretty much the latest driver.
Lockups have been reported on both Linux and BSD platforms - and given that the only fix seems to be power cycling (not just unload/reloading the driver), I doubt it's driver related in any case.