Mac Pro will not find boot volume

My Mac Pro will not find it's boot volume. Each time the computer is started, the blinking folder with the question mark is the result. A working install of 10.7 does exist on the machine's primary hard drive. If  I were to press the option key on boot, I can select the primary hard drive (after entering the password) and everything boots as normal. I have run TechToolPro on the volume with no detected errors, even after a volume rebuild. A Recovery HD partition is not on the boot volume. Should that matter?
I really really do not want to reinstall Mac OS X. I have hundreds of gigabytes of data in question. Any reinstall/reconfig would take days to complete.

So you are saying that setting the default in Startup Disk doesn't work?
And you have not got or been using Carbon Copy Cloner or another to provide working bootable backup?
You should have Lion Recovery on one of your drives, do a clean install.,
I assume TTPro media scan turns up no errors.
MOVE all your data OFF the boot drive. Keep the system OS and apps on its own drive.
Clone the system. Use TimeMachine and cloning for backup.
And how is the pram battery?
Any time you zap pram you lose the default and it will look for it like you see starting with SATA0 (bay 1)