Why does Altium delete my GND vias?

This probably happens because you have turned "Automatically remove loops" on for the GND net so whenever Altium detects that your two GND points are already connected otherwise, it will remove one of the connections to remove a loop (which admittedly doesn't make much sense for the Ground net). While placing a GND track, press TAB, make sure the mentioned option (it's somewhere in the list to the right) is deselected.