When the Loader adds  Weapon for FSX to an aircraft, it usual adds a panel.csweapon folder (i.e. another company F-16A 9\panel.csweapon), it copies then modifies the panel.cfg from the panel folder (i.e. another company F-16A 9\panel). It also modifies the aircraft.cfg, so the the panel.cfg is read from the panel.csweapon folder.

Using the another company F-16A 9 again, the aircraft.cfg is changed from this

[fltsim.0]
title=Lockheed Martin F-16A NSAWC Blue Camo
sim=F-16 F100 CAT-I
model=USA-0
panel=
sound=
texture=NSAWC_Blue
kb_checklists=F-16_check
kb_reference=F-16_ref
visual_damage=1
ui_manufacturer="Lockheed Martin"
ui_type=Armed F-16A
ui_variation="US Navy, 55, NSAWC, NAS Fallon"
ui_typerole="Single Engine Fighter Jet"
ui_createdby="another company GmbH"
description="F-16C Falcon is the Air Force's primary airspace intercepter, and multi-role strike fighter."
atc_heavy=0
atc_id=0
atc_airline=RNoAF
atc_flight_number=051
atc_parking_types=MIL_COMBAT
panel_old=

to this:

[fltsim.0]
title=Lockheed Martin F-16A NSAWC Blue Camo
sim=F-16 F100 CAT-I
model=USA-0
panel=csweapon
sound=
texture=NSAWC_Blue
kb_checklists=F-16_check
kb_reference=F-16_ref
visual_damage=1
ui_manufacturer="Lockheed Martin"
ui_type=Armed F-16A
ui_variation="US Navy, 55, NSAWC, NAS Fallon"
ui_typerole="Single Engine Fighter Jet"
ui_createdby="another company GmbH"
description="F-16C Falcon is the Air Force's primary airspace intercepter, and multi-role strike fighter."
atc_heavy=0
atc_id=0
atc_airline=RNoAF
atc_flight_number=051
atc_parking_types=MIL_COMBAT
panel_old=

This is done to every [fltsim.xx] entry in the aircraft.cfg.

Backup the aircraft.cfg BEFORE adding the weapons using the Loader, and then you can switch back to the original aircraft.cfg if it is still messed up.

Hope this helps.