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The paper I submitted was automatically processed by arXiv without a watermark. All other normal papers have the arXiv watermark on the left side of the first page.

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See the question Why doesn't my paper have the arXiv id stamped on the side of the page? from arXiv's FAQ. Stamping is not supported for submissions in PDF, docx or HTML format. For the typical case of TeX submissions, they offer two possible reasons:

TeX (and latex etc.) submissions

  1. The stamping may have been explicitly disabled. This facility is provided for journals using arXiv that wish the output to look as similar as possible to the journal version.
  2. There may be commands in the TeX source or an included macro package that write over the stamp making it invisible. This could be the result of a figure that goes to the edge of the page, or something that "clears the page". For example, using the color package and setting the pagecolor will erase the page (even if the color is white). To fix, simply comment out the \pagecolor command.
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