I have been using a previous generation mac mini server as a Windows 7 machine for the past two years without any issues. It was set up with boot camp and Windows 7 professional loaded on the internal SSD. I would like to add to the amount of disk available by using a OWC Mercury elite pro Dual Thunderbolt disk that internally stripes two 3 TB drives making a 6 TB partition. The machine boots fine with just a Mac monitor plugged in the thunderbolt. What I insert the disk into the thunderbolt chain and attempt to boot the machine the boot sequence finds the Windows 7 partition on the SSD and then the screen goes black with only a single blinking underscore in the upper left corner. The Machine and drive functions fine when plugged in using USB3. I have critical reasons for wanting to use thunderbolt instead of USB3.
OWC Brittany C: there is a limitation on using a Thunderbolt device and Windows 7. Having a Thunderbolt device plugged in when trying to boot to Windows 7 will prevent boot. Also the machine will not detect a Thunderbolt device in Windows 7 unless it is plugged in upon start up. So basically thunderbolt devices are not going to work in Windows 7. You would need another operating system on that machine in order to boot with the device plugged-in when using Thunderbolt. Or Windows 8. They fixed the Thunderbolt bug in the Windows 8.
I encountered the same problem on my Mac mini late 2012, connecting to AKiTiO Thunder2 PCIe Box with HyperX Predator PCIe Gen 2.0 x4 240GB SSD (SHPM2280P), ruuning Boot Camp Windows 2012 R2.
Here are the steps to bypass the problem:
Turn off the mac mini, and turn off the thunderbolt drive.
Turn on the mac mini, as soon you hear the boot up chime, press and hold the option key to bring up the select OS menu.
Now turn on the thunderbolt drive.
Select Windows and boot
The downside is if you restart the server remotely, it will get stuck at the boot up process. Someone needs to be physically there with the server to assist with the above steps.