What size nipples is he using? My ds went through this, he would eat about 4 oz, and then give up. I still had him on the slowest flow nipples. The minute I switched to the next size up, he went back to eating normally. He does occasionally not want the whole bottle, but I figure that is normal. But I think my ds was getting frustrated trying to suck and it not coming out as fast as he wanted!
Don't know if that is your issue, but perhaps something to think about!