By default when Batch Edit mode is enabled the user needs to click on the cell first and then change its value.
In order to help you troubleshoot the current scenario, I would need to see more details on it. Please share the markup declaration of the RadGrid and the related code-behind, so that we have a better overview of the case.
I am also attaching a basic sample showing RadGrid using GridCheckBoxColumn and GridTemplateColumn with a checkbox for you to test. It would be helpful if you modify the sample so that it reproduces the problem and send it back to us for further troubleshooting in a formal support ticket, or give us the steps to reproduce it locally.
In case you prefer to change the value of a cell by clicking directly on the CheckBox in it, check out the Editing CheckBoxes directly in Batch Edit Mode article.
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