Hello to all.
I had a very similar problem a few weeks ago. Didn't had time to much investigate it, but as I recollect:
I was shooting, and between two takes, when going into record, I had a screen warning (didn't note the exact formulation) saying something about a not existing day folder or a problem with date, I can't remember. Since there was rush, I just said OK, and went on recording.
It turned out that scene began again at 1, and since I already recorded previous n°1, n°2, etc.. scene the very morning, a A was appended to the file name to avoid name collision (since all audio files still were in the same right folder of the day).
So I had a SCENE_T01.WAV and a SCENEA_T01.WAV file, etc.. exactly as shown on the capture screen of the first post.
Just after rec, I quickly tried to play the files (new and old) and since it played back OK, I figured I would check latter the name problem.
Using Waveagent, it turned out that new files had a problematic date in metadata:
It was truncated: 27/02/201 instead of 27/02/2015.
I corrected it, as well as renumbered correctly the takes, and removed the A in the SCENE, and renamed the files.
Sorry if my post doesn't bring much information, It was too much rush to actually stop and analyse the issue, alas. But at least you know that this seems to happen for several persons.
I never encountered such a behavior before, and I just installed 1.04 firmware: it was my first shooting with it. SD card was the tried and true one, sold by SD with the 633.
Best regards.