I dont really know why this is happening to you and if you really want to do things this way wait for advice from someone else. I dont know if this works with SATA drives because ive onbly tried it on IDE drives. So look at some documentation on bootpart before you try it as well. However if you want to get Linux on a slave disk to boot from the Windows partition using the Windows bootloader (so grub doesnt mess with your windows install and you dont have to go into BIOS to boot Fedora is).
1. Disconnect the drive with Windows on it
2. Install Fedora on the Slave disk and tell Grub to install on the same disk as Fedora
3. Reconnect your Windows drive and boot back into windows
4. Get a free app off the internet called "bootpart" ftp://ftp.winimage.com/bootpa26.zip
and run it. (use the simple option for creating the boot file the Windows way)
Bootpart if run properly will put a file called bootsect.lnx on the root of your Windows C: drive and add an entry into the Windows boot.ini file pointing to it. The bootsect.lnx file then points to your grub loader so you select Fedora from a list using the Windows bootloader.
Just a quick note incase you run into the same issue I did with this program. If you try to boot into Linux and you get the error message "SYSTEM DISK MISSING REPLACE SYSTEM DISK AND STRIKE ANY KEY' just hit any key one more time and Fedora will start to load. (Hit any key twice and it will boot no worries).