I too am experiencing a timecode issue with Compressor 3. Certain video files, when uploaded to compressor and converted to MPEG2, display the wrong timecode when played in VLC or Windows Media Player. However, when played in Quicktime, the timecode is fine. There is nothing wrong with the video itself, and it plays completely from beginning to end no problem. The only issue is the timecode. It can be off by several minutes. In one instance the was wrong by almost an hour. I uploaded the same videos to Adobe Media Encoder, exported them with to MPEG2 under the same settings in that program, and did not encounter this problem. If there is an answer to this solution it would be greatly appreciated.
-Will