Safari 6 does not save the new top site

from the contextual menu. An Info dialog should open.

Back up all data. Do as above, but this time select

Services ▹ Reveal

from the menu. A folder will open with the file "TopSites.plist" selected. Move the file to the Desktop, leaving the folder open. Quit and relaunch Safari. Your Top Sites history will be empty. Test to see whether it repopulates. If it does, delete the file you moved to the Desktop. Otherwise put the file back where it was, overwriting the newer one that was created in its place, and relaunch Safari again. Post your results.

Is that the old or the new file?

Please post a screenshot illustrating the problem.

To take a screenshot, press the key combination shift-command-4. The cursor changes to a crosshair. Select the part of the display you want to show, then click. Or, to capture a single window, press the space bar and then click in the window. Be careful not to include any private information. An image file will appear on your Desktop.

Start a reply to this message. Click the camera icon in the toolbar of the editing window and select the image file to upload it. You can also include text in the reply.

From the Safari menu bar, select

Safari ▹ Preferences ▹ Extensions

If any extensions are installed, disable them and test.

Then one of your extensions was causing the problem.