To reproduce:

-Enable the course's activity completion
-Create a Upload a Single File assignment, attach a pdf or some document
-Set it to Open in a new window / popup
-Check the activity completion box to require "Student must view this activity to complete it"
-Save settings + view the course
-Switch role to student
-View the single file assignment document - a new window pops up
-The completion checkbox in the course does not get checked (until you refresh the page).

It's not really a bug in that it's working as designed, but it violates a user expectation: "I am unable to see a checked "box" beside the Course Outline even though I have viewed and printed a copy of it."

The workaround is to embed the document, which forces the course page to refresh.

Maybe there can be a JS-driven course page refresh here?

Tested on Moodle 2.6.4 and the Moodle QA Testing site (2.8 dev).