It seems like in recent missions, pilots (including myself) have reported that MAV-Fs will not reliably slave to a target designated with the FLIR.
I found at the range that I could get them to more-or-less behave properly by either;
a) press STEP to cycle to the next weapon, or
b) unselect and re-select MAVF as the active weapon.
I don't know for sure of this resets something I was doing wrong, or just clears some glitchiness, but it seemed to work pretty consistently.