I think this is a common problem for a lot of people. They don't know how to take a compliment or accept thanks. Inherently, it has to do with their own feelings of self-worth. How many people do you know when you pay them a compliment, they try to deflect it? Or when you offer thanks, they dismiss it as no big deal? Now, maybe your SO's response was a little harsher than this but I think a lot of people just feel, deep down, that they don't deserve praise or appreciation.
Honestly, based on your last two posts, I would say your SO seems to have some issues with receiving information, he has some sort of wall put up to protect himself. He doesn't seem to want to listen to your feelings(which causes him to get defensive) nor does he want your appreciation(which causes him to deflect). Is he in any type of counseling? I would suggest you trying to talk to him(since I know a lot of guys are big on 'counseling') but, as you said, I don't think that conversation would necessarily go very well.