Having trouble with combine, only some objects combine and others don't. What am I missing or doing wrong?

I've had this problem before and I can't remember what I did to get it to work. I have most of the image combined, but there are a few spots i am fighting with and they 

won't combine. They just go to the back. I've tried putting everything on one layer, I've tried numerous other things with no luck. Hoping I can get some insight here. I attached a PDF of the file. 

the white areas are what won't combine. PDF