Hi Wim,
Quoting WN
I tried your code and performed more tests. My first tests show your fix works. But than I added a \section{} in my test code and I am sorry to say that the math matrix alignment does not work at that point.
:-) Section modifies \!!counta so things get messed up again. Actually, this really helped to narrow down the bug. Basically, dostartmatrix does a test \scratchcounter=\ifnum\eqaligncolumn>\scratchcounter \eqaligncolumn \else \plusone \fi which is comparing eqaligncolmn with scratch counter, but scratchcounter is never initialized. Therefore, everything depends on what was the value of scratchcounter, which explains, different behaviour depending on when the matrix occurred, and why you had a hard time pinning down a minimal example. The fix is easy, change the scratchcounter to zerocount (or maybe just change to \ifcase\eqaligncolunm). So add this to your file, \unprotect \def\dostartmathmatrix[#1][#2]% {\begingroup \edef\currentmathmatrix{#1}% \doifassignmentelse{#2}{\setupmathmatrix[#1][#2]}\donothing \null \executeifdefined{\??mx:\mathmatrixparameter\c!location}{\getvalue{\??mx:\v!lohi}}% \mathmatrixleft \mathmatrixbox\bgroup \pushmacro\domatrixNC \let\endmath\relax \def\NC{\domatrixNC}% \def\MC{\domatrixNC\ifmmode\else$\def\endmath{$}\fi}% \global\let\domatrixNC\dodomatrixNC \def\NR{\endmath\global\let\domatrixNC\dodomatrixNC\crcr}% \normalbaselines \mathsurround\zeropoint \everycr\emptytoks \tabskip\zeropoint \eqaligncolumn\zerocount \processcommacommand[\mathmatrixparameter\c!align]{\advance\eqaligncolumn\plusone\dosetmatrixcolumn}% \scratchcounter=\ifnum\eqaligncolumn>\zerocount \eqaligncolumn \else \plusone \fi \global\eqaligncolumn\plusone \preparemathmatrix } % uses scratchcounter \protect Aditya