I don't think that the logic board RAID has anything to do with this, since the following configuration works flawlessly;
ODD 1: OS X SSD
ODD 2: Windows Boot
Sled 1-4: OS X RAID
As soon as the Windows disc is connected to the Mac Pros own SATA ports, everything works straight away.
Hard drives connected to the SIL work fine on OS X, DVD drives don't.
Booting from the SIL doesn't work either.
I don't see it as a board issue, but firmware, which isn't the same to me. The same exact board running BIOS would be fine, so I tend to view boards as hardware, even though the firmware is on it via programmable chip (it can be updated, the actual chips, and other physical components can't).
Obviously, when the Windows drive is attached though, it isn't doing so. Now I do realize it may be driver only, and do think it's certianly worth persuing. But what I'm seeing/you're describing is lending me to think it is the firmware, and is supported by all the issues others are having with eSATA cards in the '09 MP's.
BIOS emulation is supposed to allow that card to boot under Windows, and should work. So many different cards, yet none work properly. Either the drivers are extremely borked from every single provider, or the firmware is the culprit. That's the primary reason I'm thinking firmware. Better odds.
Think of it this way. You make a RAID set/s via Disk Util. That changes settings in the firmware. Those carry over to any other OS installation on the system.
From what you're telling me, the ODD_SATA ports are in fact separated as I'd expected (and hoped was truly correct). But for some reason, when the ICH's settings have been adjusted from AHCI (default value in the firmware for OS X, but not Windows) on the HDD bays (4 port group), it's causing problems it seems. I guess another thing to attempt, is while you have the Windows disk on the logic board, make sure AHCI mode is engaged.
Oddly enough, AHCI mode is capable of 0/1 RAID functions, but must be done via software. RAID allows you to get in from the firmware side (if access is there), and create an array before installing an OS to it. It also allows for a level 5, assuming enough drives are connected (Apple doesn't allow for a level 5, which is actually a good thing with software RAID, given the write hole issue).
That could well be a solution, a pretty expensive one though.
Not an option for me, as I solely use that Windows drive for gaming once in a month. All my work that requires Windows is done on virtual machines.
Definitely not cheap.
I've got the Sonnet drivers installed I guess it was me who figured out that these are working.
).
Keep in mind, there's other having all kinds of strange issues with eSATA on the '09's. Different cards won't necessarily work with the same set of drivers, and at this point, are rotating between what's available until they find one that does. It sucks.
Given the issues cover more than one make/model, it seems that the issues are more wide spread, which likely means a fundamental problem in the system (i.e. firmware, as it causes issues with multiple OS's).
The solution would either be making the card boot Windows, or making it work with the Apple CD drive on OS X (don't need that drive on Windows).
I've read a thread about making the SIL3132 work with optical drives (
http://club.myce.com/f105/sh-s203b-sil3132-boot-problems-222951/), and they say that after changing the BIOS it may work.
Sounds easy, BUT 'This download includes UPDFLASH. The UPDFLASH utility is intended for general end-users who just want to update their add-in card BIOS to the latest version. This utility is for PC add-in cards only. Do NOT use this utility for Macintosh add-in cards' [Silicon Image BIOS download].
Plus an update would require a floppy drive, which I don't have at the moment.
I've found a USB floppy drive invaluable with systems that lack an FDD port. But there may be another way.
Ultimate Bood CD (you may need to add UPDFLASH to the disk). Worth a look anyway.
EDIT:
Couple of quick questions:
1. I was under the impression you needed the eSATA card for a PM enclosure, but not sure if it's for OS X, Windows, or both. Could you clarify?
2. Would you consider using an external enclosure for the optical drive that has multiple interfaces (i.e. USB and eSATA), as you can at least have it work if eSATA isn't a possibility for awhile?
(Particularly if the eSATA card otherwise would only be needed for OS X use with the PM enclosure). Not the cleanest way to solve your issues, but inexpensive and fairly easy to do for now.