This issue is that the drawing does not have the chance to rebuild properly before saving when it is run through the task.
That explains the reason why it works when you do it manually.
Go to options for the make PDF Task in the admin tool>Output File Details>Advanced Scripting Options.
Then add swApp.Visible = True as shown below
I hope that helps.
I have that setting on and even in 2012 SP3.0 I get some PDF's of large assemblies that do not show some views