You can try add attribute auto_fill_default="Any" in the shortcode wpv-control
http://luo206.discover-wp.com/wp-admin/admin.php?page=views-editor&view_id=28
section "Filter HTML/CSS/JS":
[wpv-control field="mycustomcheckbox" url_param="mycustomcheckbox" type="select" auto_fill="wpcf-mycustomcheckbox" auto_fill_sort="asc" auto_fill_default="Any"]
see the result page:
http://luo206.discover-wp.com/how-to-search-for-checkbox-custom-field-values-using-select-dropdown/
More help:
http://wp-types.com/documentation/views-shortcodes/#vf-153286
auto_fill_default:
'text to be displayed as the default option'
optional – used to set the default value of the control. If the value is not one of the control values, the value will be placed as the first entry – good for ‘All’ or ‘Select any’ defaults.