First, let me clarify. In all my posts, I do not advocate changing the bios order to boot Windows and Linux. In fact I have taken greeat pains to recommend against this, for the same reasons that you give with your dual boot issues.
 
Let me also clarify, once again, what happens when you change the boot order in the bios.
 
1. Each OS that you install and it's ability to boot is dependent on where the drive is seen in the bios and how the drive is jumpered (IDE or pata drives) when you first installed the OS.
 
2. If you install Windows on a primary master drive and it is the first drive tagged by ther bios in the system, then the Windows boot.ini file points to the system startup files on that drive.
 
3. If you change the boot order in the bios to a second drive, that drive is seen as the first drive in the system.
 
4. You now have the second drive set first in the bios. Grub uses it's script to start the boot process (tag the boot.ini file to run Windows) on the correct drive, hd1,0, which means the master slave drive. This is correct now for Grub, but then the boot.ini file is invoked and says, "I am looking for the system files on the first drive in the system", or hd0,0. However, now this drive is really the Fedora drive, not the Windows drive, so Grub seems to hang.
 
In this case, there are two solutions, either install Grub to the MBR of hda and keep the boot order as you always had it, or "fake" grub to change the boot order of the drives when you choose the Windows boot option, so Windows boots normally (reverse mapping).
 
I am working on an article about this, for users that know how to modify the grub.conf or menu.lst file. But, this assumes that you feel comfortable with how to do this.
 
I don't use Nortons, but found this article on Norton AV.
 
If in fact, auto protection does not allow writing to the MBR, as a virus protection tool, then you need to turn off this feature, as per the instructions given, before installing any software or OS that may change any of the protected areas.

Thanks for the reply. I've re-installed Fedora, again installing grub to hda (and again it booted directly into Windows). I followed the instructions here, using the Fedora rescue disk and entering:
chroot /mnt/sysimage
grub-install /dev/hda
 
Like that thread, I got the error saying "/dev/hdb1 does not have any corresponding BIOS drive." Unfortunately, it doesn't look like a solution was found. This system is expendable, so if you have any ideas, there's not much to loose.

There seems to be a bug in Grub. I believe it has something to do with a users system and how it handles a default installation of Fedora. The grub booloader does not get installed correctly wheninstalling on a second hard drive.
 
Since this is not a mission critical system, let's try the following;
 
If you changed the bios boot order back to booting Windows 2000 first.
 
If you did a default installation of Fedora and did not specify how the second hard drive should be partitioned. This would have given you a /boot partition on the target drive and set up a LVM (Logical Volume management) partiton.
 
You know this is the caee, if you, as root user, type in;
 
/sbin/fdisk -l (the small letter L}
 
You see a small boot partition (hdb1) and hdb2 as LVM Type.
 
Get to a command line (terminal) as root user.
 
Get into grub manually and type in;
 
grub (hit the emter key & after each command below)
grub> root (hd1,0) (since fedora /boot is on /hdb)
grub> setup (hd0) (the mbr of the first hd)
grub> quit
 
Again, this assumes the bios is back to booting from the Windows drive again, before you started the Fedora installation.
 
Then reboot and see if you get both Fedora and Windows to boot.

Sweet, works perfectly. Thanks!