I had a similar problem where the checkbox had been checked, creating the key, and then being unchecked at a later time. I seemed to have fixed it with this (‘rented’ is the checkbox field):
'meta_query' => array(
'relation' => 'AND',
array(
'key' => 'status',
'value' => 'active',
),
array(
'relation' => 'OR',
array(
'key' => 'rented',
'value' => '1',
'compare' => '!='
),
array(
'key' => 'rented',
'value' => '1',
'compare' => 'NOT EXISTS'
)
)
)