When you expand the registered object in Chrome, you expand the last link to it, and not a copy of this object at the time of registration.
In your case, the last reference was to the array after the method call splice(). If you want to check the difference, you need to be more specific when registering:
var myTabs = [[0,0,0],
[0,0,0],
[0,0,0],
[0,0,0]];
console.log(myTabs[0].join(","));
myTabs[0].splice(1, 1);
console.log(myTabs[0].join(","));
You can expand it if you really want to see more.