For my second fan I just set plainly this:
M106 P2 S0
it is working as wanted now: off as standard, and can be controlled when needed.

Clarification: the fan0 is also working great, maybe I explained it wrong:

. fan0 is off
. heater1 gets to at least 45°
. fan0 starts running
. heater1 gets under 45°
. fan0 stops running

That is this line: M106 P0 S1 I0 F500 H1 T45

So except for my blown mosfet on Fan1, everything here is solved, again sorry pro3d but much much thanks for your help!

For my second fan I just set plainly this:
M106 P2 S0
it is working as wanted now: off as standard, and can be controlled when needed.

Clarification: the fan0 is also working great, maybe I explained it wrong:

. fan0 is off
. heater1 gets to at least 45°
. fan0 starts running
. heater1 gets under 45°
. fan0 stops running

That is this line: M106 P0 S1 I0 F500 H1 T45

So except for my blown mosfet on Fan1, everything here is solved, again sorry pro3d but much much thanks for your help!

@pro3d Yeah, so this works as expected now:
M106 P0 S1 I0 F500 H1 T45
Fan0 stays off untill 45° is reached on the hotend and goes off after it goes under 45° again.

Now to tackle the second one
commented all the F1 and F2 lines, and now the fan won't run, so must be a config error somewhere! (sorry for hijacking your thread like that btw, I thought I had quite a similar problem

@pro3d oh my... changed the P0 fan to H1 heater (stupid mistake) and fan0 now is off.
fan2 is still blowing 100%, but I'll look if I also made an error elsewhere.
Thanks!!!

Curious about an answer about this since I have exactly the same problem, all pwm fan keep blowing.
I suspect a blown mosfet on F1 here, but F0 and F2 just keep the fans at 100%

Config:

; Fans
M106 P0 S1 I0 F500 H0 T45
M106 P1 S1 I0 F500 H-1
M106 P2 S1 I0 F500 H-1

; Tools
M563 P0 D0 H1 ; Define tool 0

Temp on Tool 0 (Heater 1) reads 23°, so F0 shouldn't be running
Same M106 answer as pro3d