Maplex for labels is not supported. You must use the Standard Label Engine.
Labels must be created from one field in the data. You cannot create custom additions to the label using an expression parser.
Labels cannot contain a "marker text background" (like an interstate shield). It will be ignored.
Labels cannot contain a "halo" or "mask". It will be ignored.
A layer cannot use a Definition Query to limit the data shown. It will be ignored and all features will appear.
Can you please provide a list of all limitations of the Runtime Content package - possibly compared to what we are able to set up in Desktop? This list would save some time for the cartographic design folks.