Trados when used with Word has a blind spot for headers, footers and text boxes. You can go into headers manually and translate the segments, although I have heard that it is sometimes risky to do so and it is better to translate headers manually.
Tageditor is the only way around this. I dislike TE just as much as you do, but it "sees" all the text in the files, including text boxes, and it keeps ALL the formatting.
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