Adding my own two cents:
I have always loathed being complimented for "doing something right". As far as I can work out by looking back, what went on in my head was
a) They don't trust me. Doing the right thing, or doing a thing well, is the obvious thing to do so I shouldn't need to be complimented on it; it proves that they think I'm immature.
b) They're trying to control me and modify my behaviour; they aren't really happy for ME about what I just did. This is an attempt to ensure I do the same thing every time because it's more convenient for them.
As a ferociously independent child, I had much bigger issues with the effusive "Oh, well done sweetie, good job!" style of reward, perhaps because I didn't sense it as sincere (what's so WONDERFUL AND FANTASTIC about getting an A on a piece of homework? it's not like I discovered the cure for cancer). I'd second the suggestion to give a more subdued "nod and smile", as one adult to another. Sounds like your son is one who finds the act its own reward; he might feel that when you compliment him it takes away from his own personal decision to do well.