Hi,
If you got Madeira Islands (or the FS2004 patch) before November, 28, your AI aircraft are 0,5 meter above ground. If that is the case you need to get the file:
http://www.ptsim.com/downloads/af2_mad.bgl
and replace a file with the same name found at:
...\Microsoft Games\Flight Simulator 9\Scenery\Afri\scenery
Kind Regards, Luis