Quoted from Whysnow:For double elimination style events it randomly assigns byes and does so in a very strange way. Combined with this it does not appropriately use Win and Lose record to assign final position.
For example some one getting a free bye in in round one and then losing the next two rounds would end up higher than someone that won on round 1 but then lost the next 2.
Basically it provides an unfair advantage for those that get Byes.
It also messes up final place regarless of the bye. People with the same W and L in the exact same rounds can wind up with different finishing places.
I have been told it works well for single elimination but I am stilt not sure of that after seeing it fail with double elim.
The Brackelope software is fair, and without bugs. It just generates tournament brackets that certain players (like Whysnow) find unfair because they determine merit purely by Win/Loss record. The bracket affects your outcome as well as byes.
And you can get around those problems by using the Knockout format in Brackelope if the players desire.