Sorry to necropost, but I've been randomly receiving this exact same problem in Adobe Media Encoder at random times on CS6.
When doing a batch of a large quantity of files to transcode, AME will fail on a file, and every subsequent file thereafter will be 0KB. A look through the logs finds the following:
02/25/2013 12:53:38 PM : File importer detected an inconsistency in the file structure of A003_C008_1215X9_F.mp4. Reading and writing this file's metadata (XMP) has been disabled.
- Source File: /Volumes/16TB/BN-ProRes/Day 01/A003_C008_1215X9_F.mov
- Output File: /Volumes/16TB/BN-H.264-Dailies/Day 01/A003_C008_1215X9_F.mp4
- Preset Used: H264 Preview Quickrender - Mono
- Video: 1280x720, 23.976 fps, Progressive
- Audio: AAC, 160 kbps, 48 kHz, Mono
- Bitrate: VBR, 1 pass, Target 2.20 Mbps, Max 2.64 Mbps
- Encoding Time: 00:00:13
02/25/2013 12:53:38 PM : File Encoded with warning
------------------------------------------------------------
Adobe Media Encoder
Could not write XMP data in output file.
I find that the problem most consistently occurs when transcoding to MP4. File source seems to matter little by my observations, but in this case I was transcoding from 1920x1080 23.976fps ProRes.
Would dearly love to see a fix for this at some point.
System is a MacPro5,1 with 32gb of memory and a Quadro 4000. Footage is transcoding from/to a 16TB RAID array, though the problem was also happening on other storage mediums as well. I have also experienced this same problem on my personal MacBookPro9,1 at various times as well.