Allow a user to flag the same node/user multiple times
How about using the Five Star module and incrementing the rating each time?  Eg, first reply, rate the message 1.  Next reply, re-rate the message 2.  When you get to 3 (or 4 or 5) don't allow more. You could implement this directly with the Voting API if you wanted to, too, I'd imagine, if you needed higher than 5.