I have not done a dual-boot install recently, so things may have changed. However it has been my experience that Windows (any variety) gets huffy about booting if it is not the first OS on the disk. I have, in the past, had a multi-boot system with FreeBSD, Solaris, Linux and what-not installed on the same box and always had trouble unless Windows was on the first partition on the first drive. Also a third-party boot loader such as GAG was the only thing that I could get to work reliably. The FreeBSD boot loader (in the past, I don't know about now) should be installed on both disks if multi disks were involved. That (among other things) is why I went to GAG.
I believe that your boot loader is unable to find the Windows boot sector so is booting the first one it finds.
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