I'd recommend first of all repairing permissions using Disk Utility. If that fails try trashing Safari's preferences (I think just choosing 'Reset Safari' from its app menu may achieve this, if not it's in user/library/preferences, the file is com.apple.safari I think, just spotlight for it).
And if that fails try trashing the bookmarks file, it's in user/library/safari. Corruption in one of those files is probably the problem, I think it's unlikely that Safari itself has got messed up unless you installed some addons that weren't completely compatible.