How are you trying in Simplify3D? Using the slider control, sending an M106 command via communication send, or both?

What machine profile are you using in S3D? I don't remember having any issues with the profile for RepRap (Marlin/Repetier/Sprinter)

On the main S3D window, bring up Firmware Configuration under the Tools pulldown menu. What is shown on the FFF tab for fan speed control? My S3D shows M106 S$ for set fan power and M106 S0 for turn fan off. EDIT: Maybe I just don't remember setting that up. It was a long time ago.