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 :(