The only difference between the two is the current work directory at the time you call system. Does it work if you use no_chdir?

find({
    wanted   => \&tagEmacsFiles,
    no_chdir => 1,
}, "C:/Program Files/Emacs");

sub tagEmacsFiles
{
    system("etags -a \"$File::Find::name\"")
        if /\.el$/i && -f $File::Find::name;
}
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