You can set a (dynamically named) variable when you the code is executed the first time, and check for it the next.
I've been away for a long time, and a bit rusty, but this might help.

Code
ON *:TEXT:*:*:{
  // Check if the variable is set, if not then perform the rest of the code.
  if ($eval($+(%,Timeout.,$chan,$nick),2) != 1) {

    // use -u switch to unset the variable after N seconds.
    set -u3 $+(%,Timeout.,$chan,$nick) 1

    // Do whatever is supposed to happen the first time here...
  }
}

Nothing...