The script you are using is written to "do nothing" if the user is on cooldown for the command:
Code:
if ((%flooddice) || ($($+(%,flooddice.,$nick),2))) { return }

We need to tell mIRC to do something else if the user is on cooldown.

First off, you don't appear to be using "%flooddice" at all, as I am assuming that you got that from a youtube tutorial, so let's just get rid of it. Instead, I would rather first tell mIRC what to do if the user is NOT on cooldown, THEN tell it what to do if the user IS on cooldown. That just makes more sense in my brain. The ! symbol in (!$($+(%,flooddice.,$nick),2)) tells mIRC to do stuff if that vairable does NOT exist.

Code:
on *:text:!d10:#: {
  if (!$($+(%,flooddice.,$nick),2)) {
    set -u10 %flooddice. $+ $nick On
    msg $chan $nick $read(d10.txt)
  }
  else msg $chan $nick $+ , no fair, you just rolled, give the others a turn to prepare... 50DKP minus! 
}