I'm wondering if twitch also changed something so that the pipe-symbol is now being treated as the separator between 2 commands. Try changing the $(|) to use a different character to separate your commands. The closest I could see immediately would be ¦ from $chr(166) in place of $(|).

You need to be careful about using timers, as they will evaluate any word beginning with "$" as if it's an identifier. Probably a better solution would be to make a window named @Que then put your messages there instead of putting them into a timer command, then you can make an alias whose only job is to check the @Que window for any messages needing to be displayed to channel, then display them, then put themselves on a timer again if there are still remaining lines to be displayed. This way you can delay messages so they won't be flooded too quickly. My example uses a 5 second delay between Que messages. The Que window could be shared by other scripts, all they need to do is put "aline Que" in front of the message command, then call Que when they're done adding lines to the script, and Que will display the messages on a first-come/first-served basis.

Code:
alias capital return $upper($left($1,1)) $+ $mid($1,2-)
alias capital2 return $upper($left($1,2)) $+ $mid($1,3-)

on *:TEXT:!cmd:#: {
  if (%CADD.On. [ $+ [ $network ] ] [ $+ [ . ] ] [ $+ [ $chan ] ] != $null) {
    var %command_file = rcdradio_commands.ini
    var %k = $+($network,-,$chan)
    var %x = $ini(%command_file,%k,0) 
    if (!$window(@Que)) window -h @Que

    if (%x) { 
      aline @Que .msg # .w $nick == Customized Command List for channel: $capital2($chan) $+ ...
      var %text
      while (%x) {
        %kk = $ini(%command_file,%k,%x)
        var %temp $readini(%command_file,n,%k,%kk)
        if ( $len(%text ! $+ %kk => %temp $chr(166) ) >= 99) {
          aline @Que .msg # .w $nick = %text
          var %text
        }
        var %text %text ! $+ %kk => %temp $chr(166)
        dec %x
      }
      aline @Que .msg # .w $nick = %text
    }
  }
  aline @Que .msg # .w $nick == End of Custom Command List
  else {
    msg $chan I'm sorry $capital($nick) $+ , there are no custom commands currently available.
  }
  QUE
}
alias Que {
  var %que $line(@que,1)
  dline @que 1
  if (%que != $null) %que 
  if ($line(@que,1) == $null) return
  .timerQue 1 5 Que
}