WIN key not flashing properly in HS60 v1 PCB and solution

So, I’m gonna leave this here in case anyone else goes through this and I save them some time…

I noticed today that the WIN/GUI key of my HS60 v1 build wasn’t working.
After going through the usual checks, switch was fine, no shortcuts, etc, I noticed the WIN key wasn’t being flashed properly, no matter where I put it in the keyboard.
The right WIN key was even more strange, it would give me an ALT instead and the right ALT didn’t work.

No idea if this is a new thing after some QMK update, my board going silly, my particular keymap or it happens with every HS60 v1 but it’s very strange and I didn’t notice before (I haven’t used this keyboard much though).

After a few good hours trying lots of stuff I solved it by replacing the usual KC_LGUI with a null key modded by GUI. That is: LGUI(KC_NO)
You can find the same thing in the quantum tab of the qmk configurator.
I replaced the right ALT with a left ALT and that is working now as well.

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Perhaps something to do with OSX mode? Check your Bootmagic settings