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 :(
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?
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: http://technet.microsoft.com/en-us/library/cc721886(WS.10).aspx
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?
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.