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This is due to the non-standard height and depth of the MathJax fonts. Those are set to make placement of the character easier, but does have the side-effect of not highlighting the full height of the characters, as seen in your images. The v4 fonts handle this differently, so you should get better results from that, when it is officially released.
PS, the reason your extracted version doesn't show this is because you are not including the CSS that MathJax inserts into the page, and so are not getting the MathJax fonts with the atypical font metrics. Your final image is using your browser's default fonts instead.
Steps to Reproduce:
$\Sigma t = 423378$
Behold:
Technical details:
I am using the following MathJax configuration:
and loading MathJax via
This is a MathJax bug, since this doesn't happen with either raw MathML input or with extracting the rendered blob from the page:
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