A map is flat, the earth is round, therefore the map is only an approximation. The shortest distance between two points on a globe is not necessarily the shortest distance between two points on a map. Not sure that this is the reason, but it could be (4 km is small enough margin that it could be accounted for by curvature).
These close re-measures are always fun! And we think you're right! 1073 km to Malta, but 1071 km to Italy. We've lodged that update, and if Dan's microscope agrees with our one, expect to see an update :)