The issue doesn't have any relationship with GSX.
We just launch the SODE installer, which is the same as if you downloaded and installed it yourself, and the SODE installer has detected that you (by hand editing) or some other defective addon installer, has removed the default Simobject paths from the FSX.CFG, so they cannot be reliably fixed or updated by SODE to add its own folders.
Have you tried the Repair button ?
If that doesn't work, you must restore the settings of your corrupted FSX.CFG file. If you don't know how to do it, if you post it, I can point you out the error. It's in the folder listed there: %APPDATA%\Microsoft\FSX
Note that, this folder is correct only if you have only FSX:SE installed, with no FSX.