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.
Best Answer
Make sure Safari is closed when preforming this operation.
~/Library/Safari/
Bookmarks.plist
to yourDesktop
~/Library/Safari/
into your trashBookmarks.plist
in~/Library/Safari/
with theBookmarks.plist
that you saved on yourDesktop
in step 2