A checkbox field is tied to a value list. The field will be empty if no boxes are checked or have the value of the checked options from that value list.
You have to assign a value based on a value list. on the inspector on the data tab there is a section called "Values from, clicking the pencil icon you can select or create a new value list which only needs to have one value (the checked value), I use 1, when you uncheck the field the value is empty.
Actually, a check box field can contain data and yet all the check boxes will appear empty if the value in the field does not exactly match one of the values in the value list. This can happen if the data is imported into this field, edited elsewhere where a check box format was not used or if you later modify the value list without first updating the data in existing records.
A good place to explore check box fields is in "Adventures in FileMaking #2 - Enhanced Value Selection". Several layouts in this file show the same exact field with and without check box formatting so you can watch the actual data in the field change when you select and clear values by clicking check boxes in the copy formatted to use check boxes. You can also easily do that experiment for yourself just by putting two copies of the same text field on your layout and formatting only one with check boxes.