As described in #5186 and rP21675, the passability grid isn't correct on square maps for the initial players. A quick fix is to call the SetPassabilityCircular function (with false rather than true) so that square maps follow the same code path as circular maps.
Initial players:
Rejoiners:
It's probably better to have a more correct fix since the passability grid is all 1's (doesn't account for terrain) after changing the map size in Atlas, but that can be done later.