The reason why you have an FSX-SE.CFG it's because when you originally installed FSX:Steam, you still had FSX installed, so your FSX:SE has been installed in a "side-by-side" mode, so it could be used together with the standard FSX.
Then, like many users, you probably removed FSX but, of course, the FSX uninstaller, which was made so many years before the existence of FSX:SE, doesn't know anything about it, so it will not "reconfigure" FSX:Steam to run in a "stand-alone" mode.
And, FSX:SE itslelf won't "monitor" if you kept FSX installed, it will continue to run in a now useless "side-by-side" mode, even if there's no FSX anymore.
The proper way to fix this would have been:
- Uninstall FSX
- Uninstall FSX:SE
- Reinstall FSX:SE
This way, FSX:SE would have reconfigured itself to run stand-alone, so it would use exactly the same registry keys and configuration folders as the standard FSX, which is usually the easiest way to use it and it's the most compatible.
Note that, nothing of this should have any effect on GSX or any other FSDT product, because we support FSX:SE in both configurations, but not all add-on do that and, in fact, if you ALTERED the FSX:SE registry keys in some way trying to "fix" this, it's the more proper products ( like GSX, or SODE ) that will end up being confused, because you might have changed some keys, for not others.
That's why uninstalling and reinstalling FSX:SE ( being sure no trace of the old FSX is still there, both folders and registry entries ), it's the safest way to obtain a "normal" installation that doesn't have issues.