I recently reinstalled windows 7 after buying new HDD's.
My setup is 2 different raid 0's, one with the windows install and the other just extra storage space. These HDD's were bought to replace the drives that windows was on, which I why I had to reinstall.
After installing and setting up the raid on the new drives, the old storage raid (D: ) became ID 0, and the new raid (C: ) which windows was installed on is ID 1.
When I first reinstalled windows 7, the first thing I noticed was that the storage (D: ) drive was not showing up. Went into disk management and found it was due to windows not assigning it a drive letter for some reason. Changed the DVD drive to E: and set the storage to D: and all was good.
Soon after that I noticed that windows was actually booting from the D: drive despite the fact that windows was installed on C:. If I went into the bios and set C: as the first HDD, I would get an error saying BOOTMGR is missing. I think I remember D: having System and Boot as part of its properties in the disk management page.
I did some lazy research and tried doing a startup repair which didn't fix anything. Then I read somewhere about just disconnecting the other HDD when installing then reconnecting afterwards. Well rather than do that I just disabled the D: drive in the bios and reinstalled windows 7. Although disabling it in the bios didn't actually stop it from showing up as an option to install, this time it looks like everything is booting off of C: as it should be. I have C: as the first hdd and everything boots properly.
Ignore it, it will work fine as is, mine is on F: as you found changing things in bios has no effect.
The only way would be to start from scratch, disconnect the other drives leave only the one you want to install on, plug it in to ID 0, install W7 then reconnect the other drives, is it worth the trouble? probably not.