The checkboxes functionality is unrelated to the autocomplete separator. The reason for this is that we cannot predict every possible combination of properties and expected behaviors of RadComboBox when checkboxes are enabled.
What we can do in the future is to stop updating the text in the input if the AllowCustomText or EnableLoadOnDemand properties are set, although this is another not clearly defined functionality.
If you want custom checkbox behavior/functionality, please use one of the various checkbox implementations we have in our Code Library
section of telerik.com.
the Telerik team
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