What does your insert statement look like?

function insert_user_alerts($uid)
{
$message= "";
$sql= "INSERT INTO tbl_alert (nUser_Id, nNewUser, nAddFavourites,
nProfileViewed, nAddHot, nNewMessageMobile,
nNewInterestMobile)
VALUES ('{$uid}', '".addslashes($this->nNewUser)."',
'".addslashes($this->nAddFavourites)."',
'".addslashes($this->nProfileViewed)."',
'".addslashes($this->nAddHot)."',
'".addslashes($this->nNewMessageMobile)."',
'".addslashes($this->nNewInterestMobile)."')";
$res= @mysql_query($sql, $this->dblink);
if (!$res) {
$message.= "Unable to set alerts, please try later.<br>";
} else {
$this->nAlert_Id= @mysql_insert_id($this->dblink);
}
return $message;
}

The table can be updated properly. Here's that code:
function update_user_alerts($uid, $id)
{
$message= "";
$sql= "UPDATE tbl_alert
SET nNewUser = '".addslashes($this->nNewUser)."',
nAddFavourites = '".addslashes($this->nAddFavourites)."',
nProfileViewed = '".addslashes($this->nProfileViewed)."',
nAddHot = '".addslashes($this->nAddHot)."',
nNewMessageMobile = '".addslashes($this->nNewMessageMobile)."',
nNewInterestMobile = '".addslashes($this->nNewInterestMobile)."'
WHERE nUser_Id = '{$uid}' AND nAlert_Id = '{$id}'";
$res= @mysql_query($sql, $this->dblink);
if (!$res)
$message.= "Unable to update your alerts, please try again later.<br>";
return $message;
}

If I do an insert through MySQL directly it seems to populated the fields correctly.

If you pass a value in for one of those then it won't use the default. It only uses the default if you don't pass it a value.

Try changing this code ------>

INSERT INTO tbl_alert (nUser_Id, nNewUser, nAddFavourites,
nProfileViewed, nAddHot, nNewMessageMobile,
nNewInterestMobile)
VALUES ('{$uid}', '".addslashes($this->nNewUser)."',
'".addslashes($this->nAddFavourites)."',
'".addslashes($this->nProfileViewed)."',
'".addslashes($this->nAddHot)."',
'".addslashes($this->nNewMessageMobile)."',
'".addslashes($this->nNewInterestMobile)."')";

To this ----->

INSERT INTO tbl_alert (nUser_Id)
VALUES ('{$uid}')";

If a box it is not checked, it will not be in the posted values.