If the ActivePerl install is configured only by the installer, PATH modification puts the fq perl at the end of the PATH. In this case 'which perl' in msys gives /bin/perl. And gnc-fq-check fails, but gnucash builds.
If I add /c/Perl/site/bin and /c/Perl/bin to the path in profile.d/installer.sh such that 'which perl' yields /c/Perl/bin/perl, then the build fails with:
Making all in quotes
make[3]: Entering directory `/c/soft/gnucash/build/src/quotes'
rm -f gnc-fq-check.tmp
sed < ../../../repos/src/quotes/gnc-fq-check.in > gnc-fq-check.tmp \
-e 's:@-PERL-@:/c/Perl/bin/perl:g' \
-e 's:@-PERLINCL-@:C:\Perl\lib:g'
sed: -e expression #3, char 18: Unknown option to 's'
make[3]: *** [gnc-fq-check] Error 1
make[3]: Leaving directory `/c/soft/gnucash/build/src/quotes'