I've always wanted to say this "That's one sick puppy". You need to take it to the vet and see if there is something that he can fix. If not, I would recommend let that one go and find another dog.

What is the mother dog doing about it? Does the puppy nurse properly or is it the odd one out all the time?

Call your vet.

It sounds like this puppy is very sick. You said he is much smaller? He might just be hungry and his bigger siblings are pushing him out of the way. Make sure he is warmed up for about a 1/2 hour and then take the other siblings out, put him up to mom's teats (try the bottom ones nearest her legs, those have the most milk.) Allow him to nurse until he is done and put the other puppies back in. REALLY IMPORTANT - never feed or allow a feeding when the puppy is chilled. This can kill them. Warm them for awhile until their body temperature is at least 94 degrees. Have you tried supplementing him with glucose? Often times a very small puppy or a very young infant cannot produce the right amount of glycogen. If you want a formula for that, please let me know. Why are you tube feeding? If he's unable to nurse, since you said he was being tube fed, and the mom is pushing him away... it doesn't sound like a puppy that's going to pull through. Once the mother has neglected them, it's difficult to keep them alive. But - don't give up without trying. What is his stool like? Yellow, very loose stool is usually an early sign of disease. Have you tried antibiotics? Sometimes those help too. Does he have an infection where his umbilical cord was? This will get them sick very quickly. What are you supplementing him with? (What kind of formula?) If the litter is large you may also want to try cleaning his anus and penis. He may need to go to the bathroom but can't. Sometimes Mom's with large litters will neglect a puppy or two on accident. Sadly, there are just some you can't save. It's best to let them go... You can make it more peaceful for them if you remove them from the whelping box, place them in a warm box with towels and heating pads. Let them be warm. This will be more comfortable for them. When mom pushes them away they are cold and very upset. Breeding isn't for the faint of heart. You have my sympathy. I've been down this road one too many times. :( I'll be thinking about your little boy. Please keep us updated!