If you examine the 0xf7fc4380 node port on the left (the one pointed to
by 0x10ba8), you'll see that the arrows are within the node. On the
sample page, they point to the node boundary instead.
Input file: b347.dot
[erg] The change occurred before June, 2003. This is actually an artifact of the whole layout changing, so that the edge now passes through the node on its way to the port. This is the current implementation. dot does not guarantee edges to ports will not go through the node, especially as the port may be entirely surrounded by other ports.
We could provide this feature, or implement ports on ports.
Also, as noted by the submitter, the sample dot files have line breaks
in the middle of quoted strings, which means one can't run dot on
them without first fixing the lines.