When I had a similar issue on the Dreamer it tuned out to be the small tube between the extruder head and the filament drive motor. This small Teflon tube looked ok, but must have had a buildup inside as as it heated up it simply became sticky or swollen and did not allow filament to flow evenly. Depending on the filament I was using I would not hear the gear slipping, so it was as if the filament was simply not extruding.

i cleaned the tube, put it back in and no difference was seen, but eventually I replaced it with a spare I had and the printer ran like new. Not sure if the FFCP has the same tube, but I think the head unit is very similar so it may be something to look at