You should modify your code like this:
for(int i = 0; i < checkedListBox1.Items.Count; i++)
{
checkedListBox1.SetItemChecked(i, false);
for (int x = 0; x < values.Length; x++)
{
if (checkedListBox1.Items[i].ToString() == values[x])
{
checkedListBox1.SetItemChecked(i, true);
}
}
}