Are you sure your FSX:SE is configured to run side-by-side FSX ? The problem is caused because the line that adds our folder for simobjects as a SimObjectPaths line is missing, but it's supposed to be added by the installer.
However, a problem with your registry keys might prevent the installer to detect the dual install.
- Open the REGEDIT tool
- Check this folder HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator - Steam Edition
- Check the value of the Co-Existence key. If you run FSX:SE with FSX still installed, it must be 1, otherwise, if it's 0, FSX:SE is running in stand-alone mode, so the FSX.CFG used will be the one in the FSX folder instead.