Interesting stuff.. I know that FreeBSD suffered from the same issue that PC-BSD did, namely that you couldn't chainload it from a different disk (than disk 0).
Am I right in assuming that you have FreeBSD and Windows on the same hard disk? Or that FreeBSD is on disk 0 at the very least?
I might be able to find a middle ground between the two.
Do you actually see the GRUB screen? You shouldn't, and if you do, something is wrong.