PCB_BASE_FRAME::PlaceModule() calls CN_CONNECTIVITY_ALGO::Update()
on the new footprint that does not have nets assigned. The Update()
method first removes the footprint (but it has not been added, so
nothing happens) and then adds it with all pads marked as not connected.
Later, when BOARD_COMMIT is pushed - it tries to add the same footprint
again with nets assigned, but the pads are already registered, therefore
they are discarded.
To prevent this, PlaceModule() does not call CN_CONNECTIVITY_ALGO::Update()
for the just created footprint, as it is handled by BOARD_COMMIT later.