When I Place an Illustrator file inside onather illustrator file, the overprint elements failed to be overprint.
Why? Is there a bug because I use CS6, but when I tried using CS5.5 it works without any problems.
Here I created a file called single.ai, and set the text to Overprint Fill.
Here when you hide black color the orange color filled completely.
Then I created a file called Multiple, and placed then repeated it.
But as you see when I hide the black color the orange filled is etched (spoiled).
The multiple.ai file works good for me in CS6 (16.04) mac.
Though there is nothing in preferences that would affect this, I still recomend you reset them as my install is working and yours is not. In summary I believe there to be nothing wrong with the file, so the solution lies outside changing the file.