Resurrecting this zombie with new information. I just drove near this border (south on US 85 from I-94 to I-90). Curious about the mis-matched borders, I looked up the reason. Interestingly, this thread was the top Google hit. 
As this paper discusses, the border of South Dakota with Wyoming, which is supposed to be Longitude 104º W, between Latitudes 43º N and 45º N, was surveyed in 1877. The starting point was the NW corner of Nebraska. The line was surveyed northward, and measured 138 miles, 32 chains, which was within .3 miles of the calculated arc length.
The border with Montana was surveyed later (1885). That surveyor started from the presumed intersection of 27º W of the Washington Meridian with the Canadian border. He did a “random line” south, and ended up some 70 chains east of the endpoint of the prior survey. He then went back northward, setting boundary markers.
The line was re-surveyed in 1904. As it turns out, the surveyed border between Montana and SD was fairly accurate, with the SE Montana corner located at 104º 2’ W, which was also essentially the location of the monument at the 43rd Parallel (the southern border of South Dakota). Thus, it would appear that it was the surveyor heading north along the Wyoming border who didn’t get it “right”.
Of course, as usual, once the initial surveys were done, the results were accepted as the actual borders, so the 1904 re-survey did not change anything. Therefore, despite the fact that the Wyoming and Montana borders should line up, in actual fact they do not.
It should be noted that the townships of most of western South Dakota are surveyed using the Black Hills Meridian, which is the border of South Dakota with Wyoming; the baseline is located at milepost 69 along the SD-WY border. Thus, townships north of the MT-WY-SD “corner” are slightly too small, as the boundary of MT-SD is a bit too far East from that survey meridian.
It should be noted that the initial surveys were done at a time when one of the difficulties with surveying was attack by Native Americans. :eek:
For an interesting discussion of a guy who walked the entirety of the border of South Dakota, read: Boundary Walker