See next field for test.dot.
You can see the result at http://www.j-paine.org/scratch/dot_problem.wrl . The arrow that should connect p2 to a2 is in the z=0 plane.
The same problem occurs with similar dot files cntaining more arrows, when drawn as VRML. Sometimes some arrows between z!=0 nodes are in the right plane and others aren't. Similar graphs where all nodes have z=0 get drawn correctly, except that the nodes are hard to read (known bug) and that labels are missing from arrows (new bug?).
Background: I'm using GraphViz to draw diagrams in category theory, as demonstrated at http://www.j-paine.org/cgi-bin/webcats/webcats.php . I thought 3d diagrams would be particularly useful to depict "functors": functions that transform one network of relationships into a similar network. By drawing the two networks in different planes, I hope to appreciate the idea of different but structurally similar networks. Also, it's probably easier to understand such diagrams when you can rotate to view from different angles, rather than having one viewpoint into a 2d image. (I say this because your FAQ suggests avoiding 3d where not essential.)
Input file: b1449.dot
Output file: b1449.wrl