With the reputation cap, it is often the case that you "score" over the cap. Now, with reputation inconsistencies, it is often the case that it stops you from reaching actual reputation, especially in regards to the cap, from what I've seen (and please correct me if I'm wrong).
As a very simplistic solution to this problem with inconsistencies, why not add a catch of reputation after you have been capped, that can be weighed against the inconsistency in your reputation, but capped at a certain daily amount.
10 Reputation Catch per day, up to a maximum of 100 per month which is weighted 50% against the reputation inconsistency.
So, let's say I go over the reputation cap 20 days in the month, and have a reputation inconsistency of 200 reputation that month.
10 * 10 = 100 * 0.50 = 50 Reputation
200 Reputation - 50 Reputation, gives an inconsistency reduction of