Same problem with me. I shot 6 clips last saturday (SONY NEX VG20) and I wanted them in Premiere 6 CS. No audio track. I tried other clips from earlier and they were well imported as .MTS and the audio track was there.
Could it be the external mike, I used for the first time? Testclip with and without, both showed the audio track properly. With the 6 saturday tracks I could try what I wanted, no success.
Today, Monday morning I tried the entire thing on my office computer, which has very much more performance and speed. Believe it or not, the 6 clips showed the proper audio track.
I don’t know for sure if that ist the reason, but for me it seems, that lack of computer resource and speed could be the issue. That is what was manifested on my environment.