how are you trying ti engage the AP? via the F11 or by using the one that may be in the craft?
some developers disable the default built-in AP in craft that don't have one in real life...
also, you may need to check your ~/.fgfs/aircraft-data directory and remove any saved settings files for the citation... sometimes if things are changed, these saved settings get out of whack and can cause problems... make sure you are out of the sim and then delete that/those files... when you restart you should be in the craft's default configuration...