It could be the load-out. Make certain your loadout definition in the eqp file matches the loadout declaration in the cfg file of the plane's Air folder. If it is not that, then something is amiss with the Visual on the plane.
btw - this is another situation where Hebe Vollmaus's
mySH3-Tool shines in helping a modder find issues with what they are doing. His tool does not find everything you could possibly do incorrectly, but it does catch quite a bit...