I've had it work fine in several of my 10.1 DDP projects exported to geotiff using some arcpy code, and these have had some pretty complex labels in large layers. There are a lot of maplex settings you might play around with in the placement properties for a layer and within the label weight and priority settings of maplex generally. Some improve your ability to place a label, but some also would keep a label from being placed. It might be worth it to just set aside some time and manipulate different settings to see what happens. The Best setting not surprisingly works best but it is slower. If you have a lot of complex label expressions, and/or multiple classes and definition queries for them, and/or label feature weights or placement options,you can overwhelm maplex. You might also use the options to show unplaced labels in a color (default red).