When I run Print Map the layers included in the final map are not the same as the layers turned on in the viewer.

It appears the Print Map function is reverting to the default settings when the Map Services were created. That is if a layer was turned on when the service was published then that layer is included in the printed map regardless of if it was turned on in the GCX viewer. If a layer was turned off when published then it can still be turned on in the viewer but does not appear when a user selects Print Map.