In the log file of Marxan with Zones the number of connections entered does not match the actual number of connections in the boundary files. Instead the same number of connections as planning units are returned.
Short answer:
The connections are being read correctly. The printed value is wrong.
Long answer:
When changing backend implementation of how connections are stored, updating the printed value when it was changed was over looked.
The printed value prints the length of the connections list.
On previous Marxan with Zones versions, connections was just stored as a full list, so printing the size of the connections list means the full number of connections is printed.
For the current version of Marxan with Zones, connections are stored per planning unit (like a 2D representation). So the connections list is like a map – so that each pu has a list of its own neighbours. So printing the size of the connections list just prints the number of pu.