You are probably already aware of this. But lens profiles are format-specific. In other words, a profile created for raw images will not work on JPEG images. Could this possibly be a factor in your situation?
I only shoot RAW, so no.
I have defaults set per serial number, but not ISO. I never bothered with ISO defaults because I'd have too many defaults to worry about.
I'm wondering if your problem is something to do with ISO defaults, as I've never seen it. I use Nikon gear, and my raws have always had the correct lens found. I have had Auto, Default and Custom set as default lens correction setting, and the difference seems to be in the choice of vignette and distortion amounts, rather than the choice of lens itself.
I currently use Default as the (erm) default as the standard 16-35mm profile seems to overdo the barrel correction at the wide end, and selecting Auto always does the standard correction. To get what I want, I changed the distortion amount to 50, selected Save New Lens Profile Default, then Save New Camera Raw Defaults.
Now, when I open a fresh raw file, the Lens Profile starts at Default, which is 100 & 100 for all lenses (correctly found) apart from the 16-35 which is 50 & 100. Not much use to you, but I'm trying to demonstrate how it's used.
Now, if you introduce defaults for each different ISO setting, things become hard work, and you have to lots more changes. Maybe it's worth switching this off temporarily, to see if it works as expected.
You seem to have nailed it. I unchecked the ISO setting and it seems to work. I had to put each lens on the 2 different bodies and go thru the new lens profile for each. I do some more checking but it seems to pick up the correct lens. I did notice that it screwed up the rest of my default settings so will have to go back and fix them.
I checked the ISO setting to automatically apply more noise reduction at the higher ISOs. I'd rather it pick up the correct lens though. I guess I can always make a preset for the noise reduction, but it would be nice if it would work for both. I may have to open a ticket and see what happens.
I used to use presets for some of the higher ISOs. It seems like a better way to do it. Nowadays, I just do it manually.