It should be off.
M106 P0 S0 H-1
After erasing and reverting to 2.01, I decided to try 2.02 which also worked. Then I thought I'd try 3.0, it worked, 3.2, worked. And again went back up to 3.2.2 and it's still working now.
I have no idea what was causing it, I did revert to complete basics, wipe the /sys/ folder and put in just the downloaded *.g files from the reprap firmware tool. The strange thing is I didn't change my config prior to the fan issue, and 3.2.2 was initially working for me before this behavior started.
The only real difference is I did not copy the configoverride.g file back with my pid tunes and probe data, but it doesn't have anything in it that should affect the fan. It seems to be a combination of things since I definitely have a dead fet if not all fets dead on the 1.04 board, but something seemingly config related would appear to have been causing the fan not turning all the way off thing.
Gremlins at this point, I don't know.