Since it's Java, I assume there's some onClickListener function that your programmer attached to the check-boxes to update the array you mentioned. You might start by looking for that section of code, and see if it's calling the check-box object's setSelected() function to be set to True. That would force the checkbox to always be checked when you click on it.
I'm a Java programmer, so I'd be happy to look over the code and provide feedback if you want.