Very busy heading towards the Gearbox holiday week off (aka my week to work on my current project with nobody around, and some HW pokery)...
MAD file format didn't change. We still load old MAD files. I am 99.9% sure of this. HODOR is smarter than the old MAD tools though, and is better at nuking bad channels, dupe strings, etc - so an old MAD file saved will likely be smaller.
As for why a certain MAD file doesn't work - if it was made with something like CfHodEd, it could be just about anything... If I get time, I will look. But then again, every time I get free time, if I spend it looking at one person (or Mods) issue, I am not working on stuff that gets a patch out in the future. It is a hard balance to find.