I don't think it's relevant, but I have a Flashforge Creator Pro 2016.
I've noticed an issue with the cooling fan setting with changing processes over layer height. If the cooling fan is set to the same settings for all layers (off until layer 3 when printing PLA, for example), the fan shuts off during the new process and come back on two layers later. This leads me to believe Simplify3D is treating the first layer in each process as "layer 0". However, setting the fan to On for layer 0 in the new process (which starts some ways up the part) results in the cooling fan turning on when the print begins (true layer 0). I've checked the g-code to make sure the cooling fan is doing what it is told, and the commands to turn it on and off at certain heights are definitely in there.
My work around for now is to delete the cooling fan settings for each new process beyond the base one to ensure the fan stays on after layer 3. This works, but it seems Simplify3D cannot save this information to the Factory file. Opening it back up auto adds "fan off at layer 0" to all processes that have no fan speeds defined, which seems to result in the fan never coming on at all.
This issue was causing a banding issue at the layer height where the processes changed.