Add or update matrix data using PHP

We are inserting nodes via node_save. We manually enter data to $node->field_OurMatrixField['data'] before saving (paying attention to the correct column and row array keys).

If I print a $node using print_r or dpm right before saving, it looks structurally identical to a node I had saved through Drupal GUI.

Yet on insert, the [data] gets corrupted - and ends up looking like the names of my column and row headers!

Is node_save just not the way to go in this case?