Question Mark on Bootup, Goes Away Upon Restart

Hey guys,
When I boot up my workstation I get a blinking question mark and the OS doesn't load. Upon rebooting the OS will load fine.
I've tried resetting the PRAM / specifying the boot disk in 'Startup Disks' and it still keeps happening. There are no CDs / DVDs / External drives connected and I have two internal drives (the secondary was formatted before being dropped into this system).
Can I run some magical command in the terminal to tell OS X always boot off my primary?
Thanks,
~ Jon

Try things in this Apple doc.
DALE

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