I looked through Safari's entire configuration and couldn't find a single file that sounded like a likely candidate, so more or less for the heck of it, try quitting Safari, moving Yourhomefolder/Library/Preferences/com.apple.Safari.plist to your desktop, restarting your Mac, and launching Safari to see what happens. Safari will create a new file, and if your issue is corrected, you can trash the one on your desktop, and if not, you can move it back and overwrite the newly created one. (I'll concede in advance that I"m not terribly optimistic about this, but it can't hurt and may actually turn the trick.)
