Using WMFs files in PDFs can cause all sorts of problems, particularly with all or part of the WMF disappearing unexpectedly. In my experience, switching from WMF to EPS eliminates the problems.
An aside: The only time I use WMF now is if I need to give the graphics to folks who don't have the tools to edit the source files. For example, I can paste the WMFs into PowerPoint for the marketing guys. After double-clicking the WMF, it becomes completely editable (color, line weight, fonts) in PowerPoint. -Terry Smith