Yes, make sure you properly set your IRS before leaving the apron.  Nothing will work right (like the real thing) without that set.
My autopilot works absolutely perfect.  I have done several full CATIII auto lands with all three CMD lights on, LAND 3 illuminated on the AUTOLAND STATUS Annunciator and full FLARE engaged.  
If I'm not having any problems with it, then there can't be anything wrong with that feature of the software.  It must be something else.