Or you can try use this code, where the main function is made into a separate alias, and a unique name is added to each timer:
Code
on *:NOTICE:*:?: if ($regex($1-,/(.*AUTHENTICATION.*SUCCESSFUL.*)/Si) && $nick == X) { auto_join_channels }

alias auto_join_channels {
  var %i 1, %file AutoJoinChannels.txt
  while (%i <= $lines(%file)) {
    var %chan $read(%file,nt,%i)
    .timerAJC $+ %chan 1 $calc(%i * 10) join $unsafe(%chan)
    inc %i
  }
}

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