To reproduce, create a file resource (a pdf, for example) and set "Show navigation" to "Yes, without frame". Then access the resource. Look at the log and see that no record of the access appears.

We fixed the problem locally by adding another call to add_to_log in the display function in mod/resource/type/file/resource.class.php. We added it immediately after this objectframe condition

if ($resource->options == "objectframe") {

add_to_log($course->id, "resource", "view", "view.php?id={$cm->id}", $resource->id, $cm->id);