I have killed nearly every guard in solitude in front of everyone yet no bounty. I am trying to get the 1000 bounty in the nine holds achievement yet I cant obtain a bounty.

Try to do something else besides killing guards. Maybe steal something, break in houses, preach about Talos or something.

Maybe you killed all the witnesses. Othetwise I have no idea.

The guards are protecting me in white run too... Why? Is it because of the civl war or than or something?

Whiterun in my file is now a ghost town. That's one way to get them to stop protecting you.