Apparently a decision was made when creating the ListTool that setting the SelectedItemIndex when it is displaying check marks should toggle the check mark.
However, the fact that you are clearing the collection and it is maintaining the selected index sounds like a bug and I would recommend submitting the issue to the support group: http://devcenter.infragistics.com/Protected/SubmitSupportIssue.Aspx.
As a workaround, you can just get the SelectedItemIndex before setting it. If it is already 0, don't set it to 0 again.