Could my Shih Tsu have brain damage

Question
Hi Kim:
     My husband and I adopted 2 Shih Tsus approximately 5 years ago when our shih tsu of 12 yrs. passed away.  They are about 9 mos. apart and not related, but were rescued and fostered together so we took both.  
     The male is very skittish.  If you walk near him, he will run under the table.  He knows to pee and poop outside, but will still do it in the house, right in front of us as if he doesn't understand.  We always give him a treat when he does his business outside. Even when he goes out and doesn't do anything he comes running in jumping and spinning for a treat.  He also follows the other dog, the older female shih tsu, everywhere to the point that the female will try to walk away from him.  She loves him and looks for him when he's not around, but just like any male and female, enough is enough.
     He understands what "wanna go in the car" means and time for "night night" he goes right into the bedroom to go to sleep with his blanket.  He likes to play by chasing a toy and bringing it sort of back to you, at least close to where you threw it from.  
    He just seems nervous all the time.  He will not walk on grass either, maybe because he was in a puppy mill and never felt grass under his feet.  He also has a mangled ear, so I'm sure he was in an abusive situation.  He get a lot of ear infections and the vet said he has a scar in his eye.
    He has trouble jumping on the sofa and climbing up and down the stairs.  He's gotten much better but still shows signs of difficulty.  At first he couldn't do stairs at all.  I've always adopted dogs and they eventually came out of this stage, but after 5 years, he is still so worried and nervous.  I know he loves us because he will sit with us on the sofa and come in the room that we are in, but never really close.  If we have people at the house he will stay under a chair.  He doesn't understand "come" and doesn't obey any commands.  He hardly ever licks us either.  The other dog who was also rescued, from a kill shelter at  1 yr 6 months, approx. is so loveable, licks, very agile and aware of everything.  The male dog is like eyore, always seems sad unless he is getting a treat, ride or playing with his toy.  My adult children, husband and I tend to give him so much more attention because we feel sorry for him.  He will let you do anything to him too, baths, cutting hair near his eyes, cuddling with him, brushing him, taking medicine; he couldn't be more compliant but  he shows no emotion, and when we put him down he walks away. It seems crazy to say, but I work with autistic children and he seems to have many of the same tendencies.  He keeps to himself, has sensory defensive issues and not very social.  My poor baby.  We never yell at him because he would probably have a heart attack.  He's just the cutest little thing, but I want him to be happy.  I know your expertise is poodles, but any dog could have this.  Could you help me out.?  Denise

Answer
Hello Denise,
I will try to help you as best as possible.  Your dog could have had some traumatic brain injury when he was at the other facility before you got him that could be causing this.  On the good side of things, Dogs that have issues (such as blindness, missing limbs, brain injuries, etc) don't know that its not normal for them to be like that, so they don't really realize that anything is wrong.  They can go about living a more normal life thinking things are fine.  Your dog may just need some reassurance from you about certain things.  Like when you play with him, get down on his level so that you are as low as he is rather than being up above him.  With his vision problems, he might have a problem with you being over his head.  For stairs, you might put yellow tape on them where he can see it, so that its a visual aide to assist him.  Yellow Duct tape works best.  
You can teach your dog come by using a favorite treat and saying the word "Cookies".  Its not getting him to come to the word "come", but rather asking him to come to you for a goodie.  You start with him in the same room with you and you say his name and the word "Cookies".  When he looks at you, give him a piece of his favorite treat.  Praise and pet him and try it again.  You want him to stop what he is doing and come over to you to get his treat.  When he will drop everything to come to you for his treat, you can advance a bit.  Call him from a different room.  Say his name and the word "Cookies" and see if he comes running.  If he does, praise and treat him.  If not, go and show him the treat, and lead him to where you called him from and then give him the treat.  He needs to realize that he has to come to you to get the treat, not that you will go to him and give him the treat.  When he will come to you from anywhere in the house when he hears his "Cookie" word, then you can try it outside.  The same rules apply out there.  If he comes to you, great and he gets his yummy treat.  If not, you have to go get him and lead him to you.  Eventually, he won't get the treat if he doesn't come to you.  So encourage him to come with alot of praise and attention.  
You also might think about getting him into an Obedience class to help build his confidence and to help him get over his fear of people #and maybe even other dogs#.  You may want to get him in a private class first, and then introduce him to a group lesson.  This will get him started without overwhelming him.  

As for him Peeing in the house, you may need to have him wear Doggie Diapers for those times when he won't hold it.  Being in a Puppy Mill may have desensitized him to being housebroke and he may not even realize when he is doing it.  You can find "Belly Bands for Male Dogs" at http://www.bellybands.net/  

Also, as for him clinging to the female all the time, try giving each dog individual time with you, one-on-one.  This way, they each get personal time with you away from the other dog, and the other dog can have some relaxation time of their own.  During this indivual time, you can throw the ball around, take a walk, work on Obedience, or anything else your dog thinks is fun.  You might even try the Doggie Exam position with your dogs.  Especially the male.  
To do this, get on the floor with your legs in front of you.  Encourage your dog to lay in your lap on his back with his head toward your stomach.  At first just get him to relax.  Rub his tummy and talk to him until you will see his legs relax (because at first they will be straight in the air), and he calms down some.  Once he will relax, you can start the "exam" part.  You can look in his eyes, mouth, ears and over his head.  Next, look at his legs and upper body.  You are checking for anything out of the ordinary.  Next move to his middle section and finally move to the back legs and his rear area.  Get him to where he is used to having you go over his whole body.  You don't always have to do the "Exam" part, sometimes you can just rub him and get him to relax.  It is a good exercise to help him calm down, shows him that you are boss in a non-threatening way, and helps build the bond between you and him.  

I know this is alot to take in, but try a few of these things over a longer period of time to see if this will help him any.  

I hope this helps you and if you have other questions for me, please feel free to ask me and I will help as much as I can.  Good luck to your little man.