Will not start up with the selected start-up disk

I had two hard drives in my Mac Pro, a 250GB main drive and a 500GB back up drive dedicated to Time Machine. The 250GB was getting full.
I added a new 1TB hardrive and moved Time Machine to the new 1TB drive using the restore tab of Disk Utility following instructions I found on the internet, including renaming the 500 GB drive. That all worked fine.
Once I felt that was working I erased the 500GB drive and then cloned the 250 GB main drive to the 500GB drive, again using the restore tab of Disk Utility. I then changed the start up disk to the 500GB drive. It worked fine except it seemed like the white screen lasted too long at start-up.
I planned to then erase the 250 GB once I was comfortable everything was working fine.
After a few software upgrades, I found that after a shutdown, the computer would start up on the old main (250 GB) drive, which I had yet to erase, not the 500GB dive. The 500GB drive is selected as the start-up disk under system prefernces. After restart it would start up on the corrected (500 GB ) dive but now it refuses to start up on the selected 500 GB drive at all and starts up on the 250 instead, even though it is not the selected start up drive under system preferences.
Help?

Thanks for the advice.
Reboot with option and pointing to correct start-up drive did start up to correct start-up drive.
I reset the PRAM and pointed to the correct hard drive in system preferences, but upon start-up it again booted to the wrong drive.
I disconnected the USB connection to my Epson 1280 and restarted, but it started up with the wrong drive.
I then did a shut down and start up (USB connection to my Epson 1280 still disconnected) and it did boot to the correct start-up drive.
What's with that?

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