It's hard to be completely sure without more context, but I strongly suspect that Eames' answer is intended as sarcasm.
That means that meaning of the sentence as a whole is the exact opposite of the literal meaning of the words used - in this case, it would be something like "That comment was condescending, and I don't appreciate it."
'Condescension' carries fairly strong negative overtones - not just 'I think I'm better than you', but 'I think I'm better than you because you're stupid/incompetent/etc'. If Eames really did appreciate Arthur's behaviour, I would expect him to choose a different word to describe it; in this case, possibly 'Your praise is much appreciated.'
The use of that negative term, and the addition of the unnecessary phrases 'as always' and 'thank you' to the sentence, all point to the intended meaning being something more complex than just a straightforward 'I appreciate that'-type comment.
In addition, this general construction is a common response to percieved insults in English - especially to insults with a condescending tone. Sarcasm (and double-meanings in general) are often considered to be more sophisticated use of language than a straightforward say-what-you-mean response. Making a sarcastic response to a percieved insult is therefore both to show that the insult was recognised (and not appreciated) and also a signal that the speaker can use advanced language skills (and therefore an attempt to raise their own status in response to the condescension).