I'm just translating an ODT file using CT, and the header is not present in CT.
In addition quite a few spaces in the source text are replaced with tags - I assumed they were non-breaking spaces, but that's not the case. The document is badly formatted in general, so there may well be spurious tags in there, but I don't know why this has caused the spaces to go missing.
On a related point, the thing I dislike most about CT at present is the fact that it treats non-breaking spaces in Word docs (and probably others) as tags, Please change this behavior.
non-breaking spaces are displayed as such here