Dear Graham,

I have obtained the same results for

\Umathfractionnumup\displaystyle=2pt
\Umathfractionnumvgap\displaystyle=2.5pt

and

\directlua{
tex.setmath("global", "fractionnumup", "display", 131072)
tex.setmath("global", "fractionnumvgap", "display", 163840)
}

in your example in the experimental luatex 0.98.0.
I don't understand details of the problem.
Please try 0.98.0.

Best,
Akira

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