Missing Safari settings option "Safari opens with"
That option has been removed from recent versions of Safari.

I'm not aware of which exact build removed it, but I can confirm it is gone and should be gone on all clean installs of Safari on top of OS X 10.8.3 and later. After running all available updates as of May 1 - you should have Safari version 6.0.4 (8536.29.13) and no Safari opens with preference.

Unless you have a defaults write… terminal command to re-enable that setting as a hidden-features, spending time troubleshooting this would be inadvisable since the control you are looking for is gone for now.