This is normal form behavior that has nothing to do with java. You would run
into this with any server-side handler. HTML specs state that "unsuccessful"
controls do not submit to the server. An unmarked checkbox is considered
unsuccessful.

http://www.w3.org/TR/html4/interact/forms.html#checkbox
"Checkboxes (and radio buttons) are on/off switches that may be toggled by
the user. A switch is "on" when the control element's checked attribute is
set. When a form is submitted, only "on" checkbox controls can become
successful."

If you need to pass all controls regardless of success, you will have to use
hidden form fields (which will always be passed) or some other work-around.

Is it possible for you to pass whatever you need as hidden parameters,
on click of submit button.

Like for example,
document.myform.hidden1.value = document.myform.checkbox1.name;

I guess this will not work if what checkboxes you want to show on the
screen is dynamic in nature. (Eg. for a less privileged user, do not
show some checkbox). I think you can work around that, by generating
your javascript in a jsp if block.
Thanx,
SatishMotwani.