I don't know much about this particular problem buddy, but usually IF a dock vanishes, and it's set to load at startup, it 'should' reappear.. I guess it hasn't?
I'd get them the way you want them, and make sure they are set to load at startup, then do a test reboot to see if it takes? beyond that, I can't help you, hopefully someone who has had more to do with this problem than I have, can help you further, and good luck 