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