good youve solved it, mate
as to the other possible issue causing:
current airplane CFG file, always called
aircraft.cfg contents a section called
[fltsim.*] where is defined what for model will use current flight model, eg:
sim=Ju_88 //means Ju_88.AIR
model=ju_88a_4 //ju_88a_4.M3D
current airplane XDP file contents a section called
<UnitData> where is defined which m3d ariplne model is used, see for ModelName there, eg. in
ju_88a_4.xdp you will find
ModelName="ju_88a_4.m3d".
if somewhere in the game file content is such kind of naming duplicity, you can easy get problems