In both CA and GA, I have only had to turn in the form to my childrens' schools. It is kept on file and is only used if there is an epidemic, as I will be required to keep my children home.
Perry's executive order is online here:
http://www.governor.state.tx.us/divisions/press/exorders/rp65
The last clause requires parents wishing to exempt their daughters to fill out a "conscientious objection affidavit" with the state government.
I was at my allergist, and he also happens to be an immunologist, and he told me the vaccines are only 80% effective, that is, only 80% of those who get them are protected somehow. The other 20% aren't. And of the 80% the level of protection varies.