For any future scripters looking for the solution to this problem, you need to use the .setValue([array of numbers]) method instead of a simple number assignment since there are two dimensions.
{
proj = app.project;
comp = proj.activeItem;
newName = "blah";
size = 100;
newLayer = comp.layers.addSolid([0,1.0,0], newName, size, size, 1);
newLayer.name = newName;
newMask = newLayer.Masks.addProperty("Mask");
newMask.inverted = false;
myMaskShape = newMask.property("maskShape");
myShape = myMaskShape.value;
myShape.vertices = [[size*0.25,size*0.25],[size*0.25,size*0.75],[size*0.75,size*0.75],[size*0.75,size*0.25]];
myShape.closed = true;
myMaskFeather = newMask.property("maskFeather");
myMaskFeather.setValue([15,15]);
myMaskShape.setValue(myShape);
}