Here is a very simple example.
(I'm not attaching custom data on tags here but the behavior is the same...)
Using you pre-built Diagram Designer example program that came with version 2012.v1 I create a simple diagram with two shapes connected by a line.
I then save as customXml and as a customBinary.
If I then open the customXml version the shapes are present and still connected.
If I open the customBinary version, the shapes are present, but they seem to have lost the connection. Move the shapes and see the line is no long connected.
Attaching the two saved files.
Thanks,
Jason Irby