HDX and NAS and MP4

Now that I have had the software upgrade for my HDX I have added additional storage (QNAP) to allow me to get the rest of my cds on. I have created a folder called Music as the Music Store location, and am using one of the existing NAS folders to hold the dribs and drabs of downloaded music previously on my pc. I have transferred them all to this folder and most of them play fine through the HDX but everything appearing on the pc originally as MP4 even if it appears as M4a on the NAS is not being seen and is therefore not playable via the HDX. Could someone guide me in the right direction please to solve this (up to and including questioning my intelligence if it helps matters)? Thanks very much.