Code:
if ($($+(%,flood.,$nick),2)) { return }
set -u10 %flood On

This part is wrong:
if user <SomeNick1> will write something, you will create %flood for 10 secs with "On" in it, but your IF is checking for %flood.SomeNick1. You need to check for %flood or %flood.#channelname if more then 1.

Dont give a fish - teach to fish!