Why isn't my managed file getting saved?
The managed_file element handles moving the file into place and adding a file record, you don't need to save it yourself. The file module does all this in a validation function which makes the fid available in the submit handler.

So, for example, if your file element is defined with $form['file_id'] = ..., you can change your code to something like the following

$fid = $form_state['values']['file_id'];
$file = file_load($fid);
$file-&gt;status = FILE_STATUS_PERMANENT;
file_save($file);
file_usage_add($file, 'my_module', 'node', $some_nid);