Was reading a LOT of issues with Encoder CS6 not seeing audio on m2ts files upon import. I had this issue out of nowhere and was baffled as to why some m2ts files were importing with audio and some were not and was finally able to figure it out (for me anyway). I shoot on Sony AX2000's and NX5U's. When you import from camera, there are cmuprops files that accompany each video clip. I used to delete them because I didn't know what they were for. Well apparently Encoder CS6 needs them for audio. That was what was missing! The video files I imported into encoder that had audio DID still have the cmuprops files and the ones that didn't did not have the cmuprops files.
Hope this works for someone . Sure as hell kept me from pulled my hair out any more (was running out of hair!)
You should always copy the entire card to your hard drive, and never touch anything inside the folders.