Meaning of "quick reply"

Solution 1:

I look at "thanks for the quick reply" without context and it does seem as though it could have sarcastic intent to me. However, I think this could be corrected by simply changing the informality of the "thanks" for a more formal "thank you"... although if you are still uncomfortable you might use the words "speedy" or "prompt".

I'm sorry, but I think that this is largely a matter of context which could hold an almost infinite amount of sway over the final meaning of the phrase.

Solution 2:

"Quick reply" is not a special phrase. It is simply a "quick" reply. "Quick" here means:

Quick: immediate or prompt

So, it simply means a reply which was quick (prompt/immediate). Whether you appreciate someone's quick reply or not, would depend on the context of the argument. In "thanks for the quick reply", you usually thank someone for responding quickly. But it could also be used sarcastically (as I said, all depends on the context).