I had a peek at the 3DLUT cube files you shared, and this is what the raw data says. Just for the first data points.
Normalized to a 0-1 floating point scale, we get this. Since we are dealing with greyscale in these examples, going to simplify a bit and leave out all but the first color component.
The LUT is 65x65x65 (0-64), so normalizing its input is dividing by 64, and video in this example would come from 0-255, divided by 255.
Input Output
0.0000 0.0000 < actual LUT value (LUT index 0/0/0), pixel value 0
0.0039 0.0119 < pixel value 1 (1/255), LUT interpolated => Output pixel value 3
0.0078 0.0239 < pixel value 2 (2/255), LUT interpolated => Output pixel value 6
0.0118 0.0361 < pixel value 3 (3/255), LUT interpolated => Output pixel value 9
0.0156 0.0477 < actual LUT value (LUT index 1/1/1)
Looking at the corresponding screenshot above (1886 in this case), these values match exactly what the screenshot captured.
The 17 bar has an average RGB value of 3 (some dithering applies), the 18 bar 6, and the 19 bar ~10 (since the original was limited range and expansion happens, the bars are not perfectly 1 value apart either).
So ... from this it appears the LUT is applied properly. The question that remains would be if the madVR 3DLUT is just made different by the tool, or if madVR does something very different when applying it.
Can you also send me a madVR 3DLUT of the same measurement, ideally? Might be able to look at the first few values at least in a hex editor, not sure there are any tools to convert 3DLUT formats.
I was also checking ArgyllCMS for clues on how it writes LUTs, and apparently madVR LUTs are always 256x256x256. I don't think the precision makes a huge difference, but still curious.