With all drives in, try to use the windows repair. Maybe there is something strange going on with the windows loader.
I know I ran Windows with 6 Sata(3 in raid, one for windows and 2 for data) drives and no issue.
My win7 drive was unbootable. My vista drive had to boot it. I guess it saw it during install and added then entry to that drives boot manager. Maybe there is something on the other drives causing this issue.