This is very puzzling, I have an annotation feature class stored in a geodatabase that contains labels with leader lines.
The leader lines show up perfectly in the .mxd, it is only when I export to PDF that there is intermittent rendering of the leader lines. The puzzling part is that it works for some leader lines and not for others. The actually text of the annotation shows up in every single instance. A portion of the leader line stemming from the text shows up in every instance as well, it is only whether or not the leader line is completed that seems to be the symptom.
Please let me know if you need anymore info to help diagnose the problem.
Here is an example of the leader line on the left not being completed and the leader line on the right rendering correctly: