That is right, the Check List filter changes the FilterFunction to EqualTo, but you can change it back if it's no longer used. For example, as soon as clear filtering using the Check List, filter Function will get set back to Contains.
You can do that in the ItemCommand Event. Using this event, you can apply a condition to check for a specific command, then another condition that will check whether the CheckList has any filter applied. If not, that means, the check list is not in use, and therefore, switch back the filter function to "Contains":
sender, GridCommandEventArgs e)
(e.CommandName == RadGrid.FilterCommandName)
Pair args = e.CommandArgument
filterFunction = args.First.ToString();
columnUniqueName = args.Second.ToString();
GridColumn column = RadGrid1.MasterTableView.GetColumn(columnUniqueName);
 filterValues = column.ListOfFilterValues;
// if No filter is applied using the Filter CheckList
|| filterValues.Count() < 1)
// Change the Current Filter Function back to Contains
column.CurrentFilterFunction = GridKnownFunction.Contains;
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