WPF WindowStartupLocation="CenterOwner" not really center, and pops all over, why?

Probably because you didn't set the owner:

this.Owner = App.MainWindow; // for example

That's how I do it and it centers the window perfectly all the time.

To extend on what Will Eddins commented, you could create an overload method for ShowDialog() or Show() in your Window:

public void ShowDialog(Window owner)
{
    this.Owner = owner;
    this.ShowDialog();
}

public void Show(Window owner)
{
    this.Owner = owner;
    this.Show();
}

Or overload a constructor:

public MyWindow(Window owner)
    : this()
{
    this.Owner = owner;
}

If you create an extention for this, you could reuse this fine idea:

/// <summary>
/// Opens a window modally, with an owner
/// </summary>
/// <param name="window">The window to open</param>
/// <param name="opener">The owner of the window getting opened</param>
/// <returns>window.ShowDialog()</returns>
public static bool? ShowDialog(this Window window, Window opener)
{
    window.Owner = opener;
    return window.ShowDialog();
}