You know your right. Scooby is "slipping" a little on the alpha dog. Mostly due to his stroke. I think it is mostly me who can't accept it. I've always made an effort to make Scooby Alpha dog at all times. The new addition of Benji has thrown things off. She is twice the size of Scooby and Shaggy. She isn't dominant but submissive. I am in the process of getting her out of submissive mode. It isn't working very well and I am getting frustrated. Shaggy somehow has become more dominant in the mean time.
Good news/update: Scooby slept with me the other night!!! I did not know it and thought I was petting Shaggy. That is something!!!