Only one module implements hook_tokens()?
$hooks = module_implements('tokens');
print_r($hooks);


It returns the follwoing


  Array
      (
       [0] => token
       [1] => date
      [2] => domain
      [3] => entity_token
      [4] => facetapi
      [5] => logintoboggan
      [6] => name
      [7] => node
      [8] => scheduler
      [9] => system
      [10] => taxonomy
      [11] => token_custom
      [12] => user
      [13] => views
      [14] => field
      [15] => menu )


The only place which i see is it is cached, try clearing the cache or try the following

 module_implements('tokens', FALSE, TRUE)


The third params is reset to reset the cache.