I have recently run into problems with maplex label engine not being enabled on new layers. I played around in the Label Manager and that didn't work immediately. It randomly started working on the new layers 10 minutes later. I would like to know how to make sure maplex label engine is enabled for any new layers I add to future maps so I can place the labels properly. It was a Placement Properties issue I was having, only showing the default options instead of the maplex options.
You don't state which version of ArcGIS you are using, but it is possible to set Maplex to be the default label engine for new map documents. ArcGIS Help - Setting Arcmap options
If you are still having trouble, most problems can be solved by either resetting normal.mxt or rerunning your installer and choosing 'repair'.