Press ALT + R two times, look for something along the lines of:
Add
if (%flood.timer) return
inc -u2 %flood.timer
Right after it, so you have the original code with the 'on text', a new line, then the 'if (%flood.timer)...', and the rest of the code after that.
It should look something like
on *:text:*:#: {
if (%flood.timer) return
inc -u2 %flood.timer
...
}
NOTE: Do not replace the code with the above, just add a new line and paste
if (%flood.timer) return
inc -u2 %flood.timer
after it, this will limit it to one command every two seconds. You can change this by changing the '-u2' to '-u5', for once per 5 seconds, etc.