I did some looking around, in the original link:
www.rootmath.org/test/align-test
there is a difference in the MathML between the broken alignment and
the correct alignment.
//BROKEN ALIGN
====================
<math xmlns="
http://www.w3.org/1998/Math/MathML">
<mtable columnalign="right left right left right left right left
right left right left" rowspacing="3pt"
columnspacing="0.2777777777777778em 2em 0.2777777777777778em 2em
0.2777777777777778em 2em 0.2777777777777778em 2em 0.2777777777777778em
2em 0.2777777777777778em" displaystyle="true">
<mtr>
<mtd>
<mrow>
<munder>
<mo form="prefix" movablelimits="true">lim</mo>
<---- form = "prefix"
//CORRECT ALIGN
====================
<math xmlns="
http://www.w3.org/1998/Math/MathML">
<mtable columnalign="right left right left right left right left
right left right left" rowspacing="3pt"
columnspacing="0.2777777777777778em 2em 0.2777777777777778em 2em
0.2777777777777778em 2em 0.2777777777777778em 2em 0.2777777777777778em
2em 0.2777777777777778em" displaystyle="true">
<mtr>
<mtd>
<mrow>
<munder>
<mo movablelimits="true">lim</mo> <----------
the form = "prefix" is removed
This difference is present for every <mo movablelimits="true"> tag.
The broken align includes the 'form="prefix"' the correct align does
not. Sorry for the messy post, if I knew how to upload a file or
screenshot I would do that so I can point you to line numbers ect.
Thanks,
M.