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So, I've tried two different RAID controllers that have external SATA connections on my Server 2008 machine. I can install the hardware, boot into Windows, install the drivers and reboot again. No problems. However, as soon as I try to use eSATA-connected drives and reboot something happens to the Windows install and I can no longer boot into Windows. I tried repairing from the command line, and the end result is that repair console tells me I have 0 Windows installations (?). I end up having no choice but to reinstall Windows to get back on track.

I must be doing something fundamentally wrong here, but I don't know what :(

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Are the eSATA channels logically separate from the internal channels? You might be plugging two drives into a single controller and ending up with data corruption as a result.

Do you have any specific error codes? Why specifically does Windows not boot?

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You asked: "Are the eSATA channels logically separate from the internal channels?" I don't know. How can I find out? I don't get any error codes, it just boots right into the repair console. Frustrating. – Tyler Feb 12 '10 at 22:20
@Tyler, check the documentation for the RAID controller (or tell us what model it is). – Chris S Feb 13 '10 at 14:35
You might also be able to tell by going into the RAID controller's BIOS. Depending on which one, it may show drive/channel status. Or, boot off of a Linux LiveCD and see how many drives are visible. Say you have 2 internal and 2 external but when you get in there, you only see 2, you might be having the conflict Chris referred to. – ManiacZX May 11 '10 at 0:25

After you install your RAID controller and you're merrily doing your stuff in windows, but BEFORE you reboot - have you checked your boot configuration data? Here is a technet article on where to find it:

I've never seen it before, but it's possible that something having to do with the controller is screwing with it (doubtful, but it can't hurt to check).

What controller cards have you tried so far? I assume they are both from the same manufacturer?

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Windows 2008 doesn't work that way anymore. In Windows XP/2003 the boot.ini file would name a particular drive and partition by index. So if you added a new drive ahead of the one with Windows, the Windows drive would get a new index and screw things up. In 2008/Vista/7 the BCD (Boot Config DB) tells Windows to load from whatever disk was booted from (unless you modify the BCD from the default). So no matter what index the Windows disk is, BCD says to just load Windows from that disk. – Chris S Feb 13 '10 at 14:38

Can you use the automated startup repair from the DVD? It always works like a charm for Vista in this situation (disk controller changed) but I forget whether WS08 has it as well.

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