I had all the bonus medals collected but the achievement would not unlock. I looked here but nobody had a post about fixing it so I searched the web and found a solution on the Ubisoft forums. This solution was posted there by Rizzorat13 and I am passing along the information because it worked for me.
I selected an empty game save and started a new game. I went to 3 intel caches so I could unlock the location of bonus medals in the first (and easiest area). There will be 2 on that part of the map. I drove to one and rushed in and picked it up. After I picked up one bonus medal in the new game save the achievement unlocked.
It sucks that you have to do it that way but it took me about 10 minutes in total and then I went back to my main save and continued. As stated, credit for posting this on the Ubisoft forums goes to Rizzorat13. I hope it helps anybody in the TA community that is stuck.