Strange. Also not broken on all machines.
It's funny that focus map download worked in your compilation but then it doesn't work when I was testing things and tried on one of my compilations O_O I'll try to find a reason...
Regarding the dual ISO update with the code that you posted from cr2hdr (I think I took the latest from the 2), I could put everything together and it's a total mess now, but it works and it gives much better results with the highlight stripes without having to tweak the tolerances like I was doing.
The problematic video from the 5D mark III looks much better (no horizontal stripes, no shadow noise) but it flickers like crazy. It's very likely that I messed something while trying to make the updated code work. I'll take a look next weekend while cleaning things and fixing all the processing settings that are not working now

The video flicker issue:
https://mega.nz/file/l9cgDYRC#S4FmCFDKsaZD9ZNgFiToBz5Dvjzw7Kmmpo56vsGeRRkComparison from the old and the new code:

With my test clips, this is how it looks with no corrections at all (very zoomed in to see something...):

A old vs new comparison (with a bit increased highlights) to illustrate the difference, same recipe on both:

