Could it be that the changes were not saved? I believe, You have to save your changes after making the selection for them to be persisted. A good way to do this is to have a save button on the selection page.
Without knowing your domain or pages I assume the checkbox is most likely generated due to a boolean attribute in your select entity which means that value is related to the row object of select entity.
You might have to use an intermediate ui helper entity to mark which items have been selected.
The default way how the auto generated select page works is the user have to ctrl+mouse click to make a selection and then click the select button. Or double click one row to select one row object.
Hope this helps.