Hey, I am also beginning to notice this problem. I am using Publish as PDF from Visio 2007, and when opened up in Adobe Acrobat v8.1.3, only some of the shapes appear with no error. The new version of Adobe Reader does same thing plus error. But the interesting I found was that only some shapes appear.
So I started deleting shapes here and there to see if there was a problem with a shape, and I found some change
in which shapes appeared and disappeared. So I set to isolate the problem down to which shapes are causing problems.
I found almost all shapes that had angles other than 0, 90, 180, 270 would cause the error. Even an angle like 90.0001 would cause an error.
So I tried opening another PDF document generated from a file a few years back that utilized virtually the same stencil shapes. It opened flawlessly. But now when I generate the same pdf through visio 2007 from the same vsd file used originally, I get an error and the symptom of shapes appearing and not appearing.

Isolated shape that the problem comes from is attached. Three shapes are shown. Any shape drawn after the third shape will not appear.