I have had this problem several times but not every time. I get a drawing going, create a section view of an assembly or part, and the view appears correct. later if I close the affected drawing then reopen it the view will not be correct. If it is perpendicular or parallel to the parent view it will not be parallel or perpendicular, also there will be some parts missing from the assembly in the section view. I have tried opening properties and going to the hidden and hide show tabs and removing everything from that list, and I have also gone into the tree and looked to see if the parts are hidden there with no luck. I have attached a sample of what is going on here.

SolidWorks Premium 2013 sp.2 x64