It could be because of the way Weapon for FSX Loader modified the panel.cfg for the aircraft that come with Flight Deck 5.

It should have worked fine in the default CS_F-18, because that is all correctly set up in the main panel folder, but the modification to the Flight Deck 5 aircraft may have messed them up so they don't work. This has happened with other add-on fighter/bomber aircraft that I have added Weapon for FSX to, and I had to manually fix up the panel.cfg to get it to work.

Without being able to check, I can't be 100% sure if that's all that is going wrong (I don't own Flight Deck 5). Sorry.