They make me feel uncomfortable too. A large portion of me feels the compliment is undeserved (which is motivated by a feeling that I could be better than that and I should not be complimented until I am as good as I feel I could be).
Another portion of me feels like I'm being complimented for the wrong thing. For instance, when relations complimented me for receiving a first at university, I felt they were complimenting me on the vague valueless concept of a 'good grade', not out of any shared recognition of the work I had done or the complicated thoughts with which I had engaged. It felt like a nonsensical servile thing to congratulate me on it, and I was aware that it was mostly done out of politeness, as many of my relations abhor students and intellectuals, praising the far greater intelligence of 'common sense'.
Another part of me reacts because I often feel the other person could have done what I had done only if they cared enough to try. For instance, when I started playing guitar I was not very good, and I was often teased for it. My sense of rhythm was poor, and for a long time I got stuck playing everything in swing rhythm. I couldn't recognize that what I was going was swung rhythm so I couldn't stop doing it. Also my ear was poorly trained and when I tried to sing I was not only out of tune but more often than not singing the wrong melody entirely. So I was often told I should quit, because I had no musical 'talent'.
With lots of work I improved immensely. Lots of it involved ear-training, and I scarcely bothered with tabs and such at all, figuring they were 'cheat sheets'. Because of that I improved a lot in a couple of years and can now listen to a piece of music and figure out how to play it very quickly just by ear. Now I am praised, often by the same people, for having such 'talent', which they envy. They wish they had musical talent, but they don't. That irritates me because it is in fact an insult hidden in a compliment. Rather than recognizing the work you've done to become good at something, you're told you're 'naturally' like that. Which also implies they themselves have natural advantages which you yourself do not have. (As an INTP you're most often told that this is the capacity for social interaction and understanding emotion, etc.)