Hi Again
Thanks for Testing.
Now i think we get a Hardware Problem..... If you encoders NOT work in the Notepad Test then it can´t work in the Xplane Situation, too. They are simply not working basicly !
Now problem is to find out what is wrong.... Nobody Else report something like this.... And normaly Encoders should work fine !
I can´t see your Setup.... Specialy the Hardware Part.... Pretty Shure there is a Problem there, if Mobiflight completly not "see" the Encoder Inputs... OR it is a installation Problem of Mobiflight Firmware !
I can give you some tips, but again without see the System i can´t realy help you productive !
1. To check basicly if Encoder Inputs are recive by Mobiflight....
Please Enabele the Logging Mode ! Type DEBUG ( These can be done in the Settings Submenu. )
If Mobiflight is RUN and you turn a Encoder then in the Debug String ( The 3 Line Field field below the Configs) EVERY Action must be shown.
There Must be a Output like " Encoder xxxxxx execute On Right " for example. ( You can click this field and use UP/DOWN ArrowButton on Keyboard to scroll)
IF There are no notices in this Box your System NOT Get any Data from Arduino. ( Maby you can confirm while turning the Encoder the Status LED on Arduino is blinking )
Please Note.... I Not know the ArdSimX Systme.... Can you confirm the Connection from the Encoder is SAME like in Mobiflight ? In MF the Datalines (A,

bust be set to two of the DigitalPins 2-51 and the 3rd Line must be Set to GRD..... Maby ArdSim use PullUp Technic and your 3rd. Line is set to 5v ???
Or do you use a Encoder with more then 3 Lines ( With a additional 5v Power suply ??) Then you have to chekck your wire system, tot. Is that compatible to the Mobiflight Requirements ?
2. Is Firmware Update work fine ? Do you make a RESET after updating the Firmware.
Here again i not know ArdSimX.... Maby it use the EEPROM of Arduino for its firmware.... So "maby" it can be problematic to flash a Arduino as a MobiflightBoard if there is already the ARDSim Firmware in the Memmory !
If you like you can Try Out to remove the EEPROM Entrys yourself via the Arduino ID Example Sketch "ClearEEPROM" Before you try to flash the Board.
3. Can you Confirm your settings in the Device Manager are Correct.... Do you use the correct Pins for the Encoders you define in the Devices ? And Again do you make a restart after upload a Device ( Mobiflight AND Arduino Restart !) ??
Sorry i can´t help you more at the moment... It´s your job to confirm your Hardware Part is 100% Correct and you do the recommend workflows..... Only if all these is confirmed and you already get the problem we can looking for a solution !