Originally Posted by EricH (Post 1281231)

Tradition, and the FMS.

The FMS knows what the pairings called for by the Manual are--there's a bracket in Section 5.4.3. The only thing dictating the color is that FMS apparently thinks that red is the top line on any given bracket pair. Therefore, it assigns red to the higher-seeded alliance, and then the winners of the odd QFs and the odd SF.