To reproduce: please refer to the attached sample project and refer to the screenshot. You will notice that initially, the arrow is a few pixels up. If you disable and then enable the RadMultiColumnComboBox again you will notice the difference.
Workaround:

        private void radToggleButton1_ToggleStateChanged(object sender, Telerik.WinControls.UI.StateChangedEventArgs args)
        {
            ImagePrimitive img = this.radMultiColumnComboBox1.MultiColumnComboBoxElement.ArrowButton.FindDescendant<ImagePrimitive>();
            img.Margin = new Padding(0);
            if (args.ToggleState == Telerik.WinControls.Enumerations.ToggleState.On)
            {
                this.radMultiColumnComboBox1.Enabled = true;
                this.radMultiColumnComboBox1.MultiColumnComboBoxElement.ArrowButton.Padding = new Padding(0);
            }
            else
            {
                this.radMultiColumnComboBox1.Enabled = false; 
            }
        }