Although HOBBYWING 160A-HV ESC has an internalgovernor works really good,  many 3D pilots may prefer to use theinternalgovernor on their flybarless controllers.  Is there a known issue(s) or is this something that did not come up in testing? 

• The RPM signal is output from the thin yellow wire. 
• Please select the flight mode to "fixed-wing" instead of any heli mode, then the soft start-up and governor function will be realized by the flybarless controller instead of the Platinum-160A-HV ESC.  (In the fixed-wing flight mode, the programmable items of "start-up time", "Governor Parameter P", "Governor Parameter I", "Auto restart time", "Restart Acceleration Time" are all invalid)

• Please don't select "Heli (Linear Throttle)" flight mode for external governor. In this mode the ESC still has some control to the start-up RPM and the throttle response, so the ESC may cause some conflicts with the flybarless controller.

I know there is a logging feature with the Hobbywing program box. Is the logging compatible with the Jeti Jlog protocol? I have not used this personally but I know that the speed help guys are using this.

No. At this moment, it is not compatible to their system as they use different protocol