To reproduce:

public Form1()
{
    InitializeComponent();
    BindingList<Item> items = new BindingList<Item>();
    
    for (int i = 0; i < 30; i++)
    {
        if (i % 3 == 0)
        {
            items.Add(new Item(i,"Item" + i, IndeterminateBoolean.YesAndNo));
        }
        else if (i % 3 == 1)
        {
            items.Add(new Item(i, "Item" + i, IndeterminateBoolean.Yes));
        }
        else
        {
            items.Add(new Item(i, "Item" + i, IndeterminateBoolean.No));
        }
    }
    this.radGridView1.DataSource = items;
    GridViewCheckBoxColumn checkBox = new GridViewCheckBoxColumn("CheckBoxCol");
    checkBox.DataTypeConverter = new IndeterminateBooleanToggleStateConverter();
    checkBox.FieldName = "IsActive";
    checkBox.ThreeState = true;
    this.radGridView1.Columns.Add(checkBox);
    this.radGridView1.AutoSizeColumnsMode = GridViewAutoSizeColumnsMode.Fill;
    this.radGridView1.EnableFiltering = true;

    this.radGridView1.ShowHeaderCellButtons = true;
    this.radGridView1.ShowFilteringRow = false;
}

public class Item
{
    public int Id { get; set; }

    public string Name { get; set; }

    public IndeterminateBoolean IsActive { get; set; }

    public Item(int id, string name, IndeterminateBoolean isActive)
    {
        this.Id = id;
        this.Name = name;
        this.IsActive = isActive;
    }
}

public enum IndeterminateBoolean
{
    No,
    Yes,
    YesAndNo
}

public class IndeterminateBooleanToggleStateConverter : TypeConverter
{
    public override bool CanConvertFrom(ITypeDescriptorContext context, Type sourceType)
    {
        return sourceType == typeof(ToggleState);
    }
    
    public override bool CanConvertTo(ITypeDescriptorContext context, Type destinationType)
    {
        return destinationType == typeof(ToggleState);
    }

    public override object ConvertFrom(ITypeDescriptorContext context, CultureInfo culture, object value)
    {
        if (value is ToggleState)
        {
            switch ((ToggleState)value)
            {
                case ToggleState.On:
                    return IndeterminateBoolean.Yes;
                case ToggleState.Off:
                    return IndeterminateBoolean.No;
                case ToggleState.Indeterminate:
                default:
                    return IndeterminateBoolean.YesAndNo;
            }
        }
        else
        {
            return base.ConvertFrom(context, culture, value);
        }
    }
    
    public override object ConvertTo(ITypeDescriptorContext context, CultureInfo culture, object value, Type destinationType)
    {
        if (destinationType == typeof(ToggleState))
        {
            if (value is IndeterminateBoolean)
            {
                switch ((IndeterminateBoolean)value)
                {
                    case IndeterminateBoolean.Yes:
                        return ToggleState.On;
                    case IndeterminateBoolean.No:
                        return ToggleState.Off;
                    case IndeterminateBoolean.YesAndNo:
                    default:
                        return ToggleState.Indeterminate;
                }
            }
            if (value is string)
            {
                switch (((string)value ?? string.Empty).Trim())
                {
                    case "Yes":
                        return ToggleState.On;
                    case "No":
                    case "":
                        return ToggleState.Off;
                    case "Both":
                    default:
                        return ToggleState.Indeterminate;
                }
            }
            else
            {
                return base.ConvertTo(context, culture, value, destinationType);
            }
        }
        else
        {
            return base.ConvertTo(context, culture, value, destinationType);
        }
    }
}

Workaround: use the custom filtering functionality: http://docs.telerik.com/devtools/winforms/gridview/filtering/custom-filtering

You can access the RadGridView.FilterDescriptors collection and according to the FilterDescriptor.Expression property to determine whether the row will be visible or not.