Using the configurator (configurator.reprapfirmware.org), I ran into an issue with the thermostatic control for fans. (as of 15 April 2018)
After digging, it turns out that the configurator was not generating the correct gcode.
I have a 2 hotend machine, when setting Fan 1 to E0 & Fan 2 to E1, (threshold at 45C) the gcode was as follows:
M106 P1 S1 I0 F500 H T45
M106 P2 S1 I0 F500 H T45
The gcode that makes things work for me was:
M106 P1 S1 I0 F500 H1 T45
M106 P2 S1 I0 F500 H2 T45
Full details for the M106 command can be found here.
I hope anyone having issues with thermostatic controlled fans finds this useful.