To reproduce:
1.Add a GridViewCheckBoxColumn and populate the grid with data:
radGridView1.DataSource = Enumerable.Range(1, 100).Select(i => new { Check = i % 2 == 0});
2.Add a RadButton and on its Click event clear the filters:
private void radButton1_Click(object sender, EventArgs e)
{
    radGridView1.MasterTemplate.FilterDescriptors.Clear();
}
3.Run the application and change the filter to show only checked items. Then click the button. The check box in the filtering row for GridViewCheckBoxColumn was not updated properly.

Workaround:
this.radGridView1.BeginUpdate();
radGridView1.MasterTemplate.FilterDescriptors.Clear();
this.radGridView1.EndUpdate();