When a recipe states a target for all grain it is different from extract. Equipment can be different, water can be different, and especially the grind of the grain can be different. There are many factors which influence efficiency. What is most important is to be consistent. It may be that you just need to use some more base malt based on your set up, grind, etc.
Also, your post is a bit confusing. you say you are missing your FG but the numbers you posted, 1.061 and 1.053 are post boil/pre-fermentation gravities. Lower than expected post boil gravities are an indication of lower efficiency while lower FGs would be an issue with fermentation.