Here are two possible causes for what you are observing:
If you format a field to give it two or more check box values, FileMaker will store each value you select as text, separated from other selected values by a return character. The order of the listed values is determined by the order in which the checkboxes were clicked. If you click the last check box and then the first check box value, the last check box value will be listed first if you examine a copy of the field formatted as an edit box.
In an edit box formatted copy, each such value will be on a different line of text in the field. Thus, an edit box formatted copy of the field may not show all selected values if it is not tall enough to show all rows of text. You may have to click/tab into the field to see all the values entered into it.
When you format a field with check boxes, any data present in the field that does not match one of the current values in the value list specified for it will not show in the field when formatted with checkboxes, but will show if you format it as an edit box. Thus, if your field used a value list of two values: apple; orange, you might have "lemon" entered in the field and it won't show in the check box formatted copy of the field.
Also, if you edit the value list to change the values listed, this does not have any effect on what data is already stored in the field. As just described in the previous paragraph, any such data that no longer matches one of the values in the value list is now invisible in the check box formatted copy of the field, but will still be visible in the edit box formatted copy.