The colors don't change because you actually create new buttons and give them a color. What you can do instead: put the buttons in an array, loop over the array and change the color:
Button[] buttons = new Button[] { button1, button2, button3, button4, ..., button15 };
for (int i = 0; i < buttons.Length; i++)
{
Button currBtn = buttons[i];
currBtn.BackColor = Properties.Settings.Default.cColorBack;
currBtn.FlatAppearance.BorderColor = Properties.Settings.Default.cColorFore;
currBtn.ForeColor = Properties.Settings.Default.cColor;
}