Trusted Root certificates regularly disappear on Windows 7

"Root" store solved it

The solution was to install it into the Root store, which puts it under Registry (if you view physical stores in the Certificates snap-in), instead of the AuthRoot store, which puts it under Third-Party. I don't know why it was disappearing from Third-Party, but it hasn't happened since I made this change.

Thanks to Charlie Wilson for pointing me in the right direction. I just wanted to type out the full answer in case anyone else had this problem.

When you choose where the certificates should be stored are you choosing a physical store such as Registry or Local Computer? I am not sure what the problem is but I have always been successful with choosing Registry. Good luck.