Ok I found the issue was the reg entries that were to be delete were not being deleted. So I removed them out that fix the duplicate message. In my .ini file under joystick I'm getting "missing joystick" message but everything else is ok. I image its one of my reg entries for joystick but I can't tell which one it is.
[JoyNames]
AutoAssignLetters=Yes
0=X56 H.O.T.A.S. Throttle
0.GUID={0F856C10-889C-11EB-8001-444553540000}
1=T-Rudder
1.GUID={7CCBF530-0A68-11EB-800E-444553540000}
2=X56 H.O.T.A.S. Stick
2.GUID={0F856C10-889C-11EB-8003-444553540000}
A=X56 H.O.T.A.S. Throttle
A.GUID={0F856C10-889C-11EB-8001-444553540000}
B=T-Rudder
B.GUID={7CCBF530-0A68-11EB-800E-444553540000}
C=X56 H.O.T.A.S. Stick
C.GUID={0F856C10-889C-11EB-8003-444553540000} D=<< MISSING JOYSTICK >> << MISSING JOYSTICK >>
********* FSUIPC7, Version 7.0.6 (10th March 2021) by John Dowson *********
Checking for FS path in 'C:\Users\steva\AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache\UserCfg.opt'
FS path found = E:\Games\Microsoft Flight Simulator 2020\
WebSocket server found: E:\Games\Microsoft Flight Simulator 2020\FSUIPC7\\Utils\FSUIPCWebSocketServer.exe
Windows 10 Pro 64 Bit reported as Build 19042, Release ID: 2009 (OS 10.0)
Reading options from "E:\Games\Microsoft Flight Simulator 2020\FSUIPC7\FSUIPC7.ini"
Checking the Registrations now ...
FSUIPC7 Key is provided
WIDEFS7 not user registered, or expired
79 System time = 19/03/2021 10:15:43
79 FLT path = "C:\Users\steva\AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalState\"
110 -------------------------------------------------------------------
125 Registered HotKey 'InvokeFSUIPCOptionsKey' (key=0x46, modifier=0x1)
157 FS path = "E:\Games\Microsoft Flight Simulator 2020\"
157 ---------------------- Joystick Device Scan -----------------------
157 Product= T-Rudder
157 Manufacturer= Thrustmaster
157 Vendor=044F, Product=B679 (Version 1.16)
204 GUIDs returned for product: VID_044F&PID_B679:
204 GUID= {7CCBF530-0A68-11EB-800E-444553540000}
204 Details: Btns=0, POVs=(0, 0, 0, 0), Cal=x00000000, Max=R0,U0,V0,X1023,Y1023,Z1023
219 Product= Saitek Pro Flight X-56 Rhino Throttle
219 Manufacturer= Mad Catz
219 Serial Number= k0003507
219 Vendor=0738, Product=A221 (Version 1.0)
219 GUIDs returned for product: VID_0738&PID_A221:
219 GUID= {0F856C10-889C-11EB-8001-444553540000}
219 Details: Btns=36, POVs=(0, 0, 0, 0), Cal=x00000000, Max=R255,U255,V255,X1023,Y1023,Z255
219 Product= Saitek Pro Flight X-56 Rhino Stick
219 Manufacturer= Mad Catz
219 Serial Number= k0023297
219 Vendor=0738, Product=2221 (Version 1.0)
219 GUIDs returned for product: VID_0738&PID_2221:
219 GUID= {0F856C10-889C-11EB-8003-444553540000}
219 Details: Btns=17, POVs=(0, 0, 0, 0), Cal=x00000000, Max=R4095,U255,V255,X65535,Y65535,Z0
219 -------------------------------------------------------------------
219 Device acquired for use:
219 Joystick ID = 1 (Registry okay)
219 1=T-Rudder
219 1.GUID={7CCBF530-0A68-11EB-800E-444553540000}
219 Device acquired for use:
219 Joystick ID = 0 (Registry okay)
219 0=X56 H.O.T.A.S. Throttle
219 0.GUID={0F856C10-889C-11EB-8001-444553540000}
219 Device acquired for use:
219 Joystick ID = 2 (Registry okay)
219 2=X56 H.O.T.A.S. Stick
219 2.GUID={0F856C10-889C-11EB-8003-444553540000}
219 -------------------------------------------------------------------
282 LogOptions=00000000 00000001