When I assign a prefix using prefix settings - user- - I fill out a special prefix my company uses
(could be anything letters numbers example  D1) for all the part types but for some reason the prefixes never show up for MAIN PART folded plate or folded beam.  in as 2011 it only did this with the folded plates.

Here is what I click to clear any confusion.  
prefix settings tool > User (expand) > Default (expand) > Beam (expand) > Any, then I put my prefix in assembly on the right.  I do this for all the types listed under default.    

Can you try and see if a folded plate folded beam MAIN PART gets a prefix?
Thank you