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Are you sure your input format is set correctly? I run into this problem because sometimes while I mean to convert from pdf to epub, Calibre sometimes changes the input format automatically to epub when one exists from a previous conversion as that's one of my preferred formats.
The other bit is if it's not being highlighted it's probably because of the [] characters in your title. You need to escape those with backslashes \[ \].
That footer is hardcoded into preprocessing because it's pretty universal in the way it's formatted.
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