Ok this is a bug and I fixed it myself. Please include in the next release!
The issue was not considering, that empty checkboxes return nothing and need to be saved as well.
Here what needs to be changed:
File user-meta-manager.php
Lines from 1734 to 1741:
CHANGE FROM:
foreach($show_fields as $field => $field_name):
if(isset($_POST[$field_name]) && array_key_exists($field_name, $umm_data)):
$posted_value = addslashes(htmlspecialchars(trim($_POST[$field_name])));
$val = (is_numeric($posted_value)) ? sprintf(“%d”, $posted_value) : sprintf(“%s”, $posted_value);
$output .= $field_name . ” = ” . $val . “\n”;
update_user_meta($current_user->ID, $field_name, $val);
endif;
endforeach;
CHANGE TO:
foreach($show_fields as $field => $field_name):
$posted_value = (isset($_REQUEST[$field_name])) ? addslashes(htmlspecialchars(trim($_REQUEST[$field_name]))) : ”;
$val = (is_numeric($posted_value)) ? sprintf(“%d”, $posted_value) : sprintf(“%s”, $posted_value);
$output .= $field_name . ” = ” . $val . “\n”;
update_user_meta($current_user->ID, $field_name, $val);
endforeach;