So, I promised that I would get to the bottom of the real story and report back here with my findings.
I have asked several people in this office who have been here much longer than me (wow, that's impressive, they've been here longer than 3 months), and they all have answered with "no, but I've heard stories" (and all of the stories are similar to what we have already discussed).
As I suspected, there is no real mystery as to what happened. There was no "mix-up" with the shipment of the brick and limestone. There was no "mix-up" of the plans at the State level.
The drawings (I looked at them in the Facilities Planning archives) are clearly for a "Men's Dormitory at Kansas State College" (Goodnow was the first of the three buildings). The plans also clearly call for the red brick veneer that you see prominently displayed to this very day.
The architect was Ekdahl, Davis, Depew out of Topeka. This really doesn't matter all that much, but I am blaming them for designing and presenting something so obviously not in line with the look of the rest of campus. I don't know what their actual charge was when they were given the job, but I give them a huge FAIL.
I also have to lay some blame with the University Architect for KSU at that time (no idea who it was), for allowing such an albatross to be constructed (not just one, but THREE).
One other thing that was mentioned when I was asking around about this was that the appearance could have been an attempt to match the appearance of Jardine Terrace. I guess Jardine came before Goodnow, and since they were both (at that time) at the far edges of campus, they may have been trying to pull off a common look.
I was told yesterday that there are dorms at KU (and someone else mentioned this in the other conversation) that are exactly like Goodnow and Marlatt. He told me they were all designed and built at the same time. I suspect that the State of Kansas, in their infinite wisdom, decided to save a buck by paying one architect to design a dormitory, and they would use that same design on both campuses. Nevermind that the two campuses have two completely different architectural styles.
So, like most crazy stories, turns out there is no real story there. It is much more fun to continue the stories that we have all been told throughout the years.