Code:
alias test {
  inc -u5 $+(%, no., $nick)
  if ($($+(%, no., $nick), 2) >= 3) {
    echo -a CTCP flood detected from: $+($nick,$chr(44)) %ctcpflood ctcp's in %ctcpftime seconds. $+($chr(40),ignored,$chr(41))
  }
  if ($cexcctcp == $true) || ($readini(settings.ini,protection,ctcp) == Disabled) { 
    echo -> rest of the code here
  }
}


Simple matter of placing your commands/if statements in a slightly different order.