Rules (not) triggered with Bulk Media Upload
As noted, your rule is setup for serial upload operations; BMU sets the entities in a batch process, rather than one reference/file at a time. 

You may be able to overcome the race condition resulting from the rule firing and batch processing by triggering the rule on node save rather than individual file uploads while editing the node.  This will ensure each file has a Drupal FID assigned and has been fully added to the files table in Drupal for referencing.