It does seem to be a case of one or the other. I can get Weapon for FSX to work in FSX-SE, on my PC, but not the Loader. This is after copying it from FSX to FSX-SE.

On my laptop, I only have FSX-SE installed, and Weapon for FSX, including the loader, work fine.

When only FSX-SE is installed, it creates an FSX folder in the %AppData%/Microsoft (C:\Users\<yourusername>\AppData\Roaming\Microsoft) folder, and everythyhing works fine because of it.
However. When you have both installed, FSX-SE creates an FSX-SE folder in the %AppData%/Microsoft (C:\Users\<yourusername>\AppData\Roaming\Microsoft) folder, and I'm pretty sure that's where products only made for FSX end up with problems (see attached image).

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