This can definitely happen when formatting from .doc to .docx file as .docx which stores the file in Open XML Document format. My best guess at your situation is that some of the formatting changes are being lost in translation.
There is no real way around this as I have seen this in the past with some of the documents I have updated.
One suggestion is that you could try an online .doc to .docx converter and see if there are any differences.
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