@EthanBrown has already pointed out the problems. Here is a solution that puts all the logic in the constructor, and avoids the problem of pushing the instance after having it created from a wrong number.
function GroupData(parentnum) {
this.parentnum = parentnum;
this.refnum = GroupData.colorGroup.length;
GroupData.colorGroup.push(this);
if (GroupData.colorGroup.length < 5)
new GroupData(this.refnum);
}
GroupData.colorGroup = [];
var root = new GroupData(0);
alert(GroupData.colorGroup.length+", "
+GroupData.colorGroup[GroupData.colorGroup.length-1].parentnum);