Okay. Do this.

Add the weapons to the aircraft using the Weapon fort FSX Loader. Back up newly created panel.csweapon folder and the CSWeapon.xml. I usually add them to a Zip file.
Once backed up, remove the Weapons from that same aircraft using the Loader.
If you zipped the panel.csweapon folder and CSWeapon.xml, unzip them back into the aircraft folder.
Now add a new variant of the aircraft (using method 2) and it should then work.

I often add Weapon for FSX to my aircraft manually, rather than using the Loader, so I know it will work. ;)