Changing your check box field's value list values, does not change the data already stored in the field.
It sounds like your field may be storing values that no longer match an item in your current value list. If that's the case, the data is still there, but the check box formatting hides these values from view. To check for this, place a copy of your check box field on your layout next to the original copy and set it up as an edit box. Now inspect the contents of this field for data that doesn't match your current value list.
If you need to update this field for large numbers of records in order to correct the problem, make a back up copy of your file and try out the Replace Field Contents tool in the Records menu.
How do you set it up as an edit box. Im super new to this, and as a intern for this company this is the sweetness that i get to deal with.
An edit box is the simple unformatted field.
Enter layout mode.
Simply copy and paste the existing field or duplicate it.
If using filemaker 10 or older, use field / Control | Setup... to change the copied field's format from "Check boxes" to "Edit Box".
IF using FIlemaker 11, this option is found in the inspector.
After doing this, you may want to "play" with the fields by clicking check boxes and noting how the data in the unformatted copy changes--that can be instructive.