The problem I am having seems to originate in FCP when sequences are inexplicably exported without timecode (programs should start at 09:58:30:00, for example, and when exported start at 00:00:00:00). From a batch export of ten sequences, one might end up without timecode for no obvious reason. The same asset, with no changes to settings or filename, can be re-exported and will have the correct timecode embedded.
Lack of timecode is almost always accompanied by the filename being changed automatically during export. For example if a sequence is named 'Sports show 1' in FCP then it might be spat out as 'sports#1DAA3C'. This can often occur when the original filename is too long, but not always. I have noticed a couple of other threads that discuss this issue but none seem to ever reach a conclusion. Timecode is crucial for transcoding in either our Digital Rapids or Rhozet.