Check if both pilots have exactly the same version of X-Plane and the same scenery, meshes, and airports installed!
SmartCopilot plugin synchronizes absolute elevation coordinate (aka distance from the middle of the Earth). If both pilots have different scenery installed, it could happen that the earth level above the see could be different at the point.
If you are not sure which scenery you have, open X-Plane log file (Log.txt) and check following lines on both sides:
I found the following scenery packages (prioritized in this order): 0 Custom Scenery/KLAS Las Vegas Mc Carran/ 1 Custom Scenery/Aerosoft - EBBR Brussels/ 2 Custom Scenery/Aerosoft - EDDF Frankfurt/ 3 Custom Scenery/Aerosoft - EDLP Paderborn-Lippstadt/ 4 Custom Scenery/Aerosoft - EGLL Heathrow/ 5 Custom Scenery/Aerosoft - LFMN Nice Cote d Azur X/ 6 Custom Scenery/Aerosoft - LFPO Paris Orly/ 7 Custom Scenery/Aerosoft - LPFR Faro/ 8 Custom Scenery/Aerosoft - LSGG Genf/ 9 Custom Scenery/LOWI Demo Area/ 10 Custom Scenery/Global Airports/ 11 Custom Scenery/KSEA Demo Area/ 12 Global Scenery/X-Plane 11 Demo Areas/ 13 Global Scenery/X-Plane 11 Global Scenery/ 14 Resources/default scenery/1000 autogen/ 15 Resources/default scenery/1000 decals/ 16 Resources/default scenery/1000 forests/ 17 Resources/default scenery/1000 roads/ 18 Resources/default scenery/1000 urban terrain/ 19 Resources/default scenery/1000 world terrain/ 20 Resources/default scenery/700 roads/ 21 Resources/default scenery/900 beaches/ 22 Resources/default scenery/900 europe objects/ 23 Resources/default scenery/900 forests/ 24 Resources/default scenery/900 roads/ 25 Resources/default scenery/900 us objects/ 26 Resources/default scenery/900 world object placeholders/ 27 Resources/default scenery/airport decals/ 28 Resources/default scenery/airport scenery/ 29 Resources/default scenery/default apt dat/ 30 Resources/default scenery/default atc/ 31 Resources/default scenery/sim objects/ 32 Resources/tutorials/tutorials_Alaska/ 33 Resources/tutorials/tutorials_Hawaii/ 34 Resources/tutorials/tutorials_Seattle/