Why does my Mac Pro try to start up from a blank drive?

I fitted a 2nd drive to my 2006 Mac Pro in anticipation of dual booting Windows (not done yet). The dive is FAT formatted but is empty. Why does the Mac Pro try to boot up from that drive every time I start it up, despite having set the startup disc as OS X in the System Prefs?! Getting sick of seeing the flashing folder with the question mark evry time I start it up.

I might be inclined to think the problem is really on your startup drive. You might try reinstalling Snow Leopard.
Also, try:
Resetting your Mac's PRAM and NVRAM
Reinstall OS X without erasing the drive
Do the following:
1. Repair the Hard Drive and Permissions
Boot from your Snow Leopard Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer.
If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
2. Reinstall Snow Leopard
If the drive is OK then quit DU and return to the installer.  Proceed with reinstalling OS X.  Note that the Snow Leopard installer will not erase your drive or disturb your files.  After installing a fresh copy of OS X the installer will move your Home folder, third-party applications, support items, and network preferences into the newly installed system.
Download and install the Combo Updater for the version you prefer from support.apple.com/downloads/.

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