you might have two of these like your old one and the new one, but have clicked the old one?
I tested again using the milisecond timer and have no trouble
Code:
menu status,menubar {
  Test It
  .Do Testit: {
    set %x 1
    while ( %x <= 3) {
      TIMERmsg $+ %x -m 1 3000 /msg $me %x
      inc %x
    }
  }
}

results were
* Timer msg1 activated
* Timer msg2 activated
* Timer msg3 activated
* Timer msg3 halted
* Timer msg2 halted
* Timer msg1 halted

changing back to a nonmilisecond timer the results:
* Timer msg1 activated
* Timer msg2 activated
* Timer msg3 activated
* Timer msg1 halted
* Timer msg2 halted
* Timer msg3 halted

note the order in which they fire? I don't know that it matters to you
or not.