Ah!
Thank you Hendrik, that is very interesting. I don't think I ever knew about the soft telecine concept.
That makes a lot of sense, and corresponds with what I was seeing, not only mathematically, but also in terms of content: only some of my files exhibited this behavior, but all the ones that did were SD-DVD rips of movies. So indeed, all of that original content would have been at 24fps, and then on some they fudged the DVD release with the process you describe. Other SD-DVDs that did not exhibit this behavior were obviously mastered differently.
One thing that confused me was that despite the large number of dropped frames, I was not seeing any obvious visual defect. They seemed fine, as you said, and so are probably working as intended.
The contradiction between the two repeated frame calculations in the MadVR OSD was doubly confusing. But I guess that if the repeated frames are "expected behavior" when MadVR encounters soft-telecined source material, it doesn't include that in the calculation up top, but does included it in the bottom count anyway. To me that's confusing behavior, but ok.
Thanks so much for educating me on this.
I've found that if you open the file in MPC-HC and look at the MediaInfo, it will show a frame rate of 23.976 for a file that doesn't have this issue, but 29.970 for one that does (which must be the Soft Telecine). JRiver (also VLC) thinks both files have a framerate of 29.97, of course.
Thanks!