...further reading reveals that there was indeed problems with the cold and dark scenario shipped with the FSX version....
However an update was released pretty quick, and it sorted a number of other issues reported in the PMDG support forums, which also went for the fs9 version. It fixed issues with the -400F as well...
Did you get this update? Im assuming so

The alignment time can be altered in
options to speed it up, but it depends on how realisitic you want your pre start checklist to be.