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
