It's not so much repeating segments as large solid areas. Since they always match at any overlap point, you need to increase the minimum match percentage so it will have to match the other parts of the map as well. There's no optimal settings for every game, you should expect to tune it for every game or even different parts of each level, in the trickier cases.
A more intelligent matching algorithm would try to detect features and match them across frames. This might even be faster than my brute force method, and would not be affected by blank areas.
