I have used Spartan 3 FT256 generated 13 pairs differential output signals.
They are laid out on PCB with the same separate distance and length in each pair is same.
Right now the problem is that the positive and negative polarity output of one pair signals close to the middle of the group is not 180 degree shifted. Looks like they are 90 degree shifted.
Also check your PAR pad summary or use FPGA Editor to be sure the pair is connected to a normal differential driver, instead of somehow connecting to independent drivers.