Maybe I'd find this subtly humorous too, if I read it in context -- but I don't know this particular book of hers. But I don't have any trouble imagining myself, or anyone else, using this tense in this sentence. I'm going to give my interpretation of the two sentences, but in reverse order:
You agreed to send the check two weeks ago, but it hasn't arrived yet.
Earlier in this same conversation, you agreed to do something -- but since that something was supposed to happen two weeks ago, this tense doesn't jive.
You had agreed to send the check two weeks ago, but it hasn't arrived.
The last time we spoke about this (i.e. two weeks ago), you agreed to send the check; but evidently you didn't send it.
As you probably know, the past perfect is used when there are two different points of time in the past that we want to talk about. For example, "The snow plow had already come through when I got up this morning."
They forged an agreement in the the distant past, and then the person's way of thinking about sending the check changed at some point. He or she did an about-face in the more recent past.
Also, "You agreed" sounds more accusatory to my ear -- kind of like "you lied." It's subtle.