To answer a few questions...
About bias: The director of gifted ed didn't go into detail, but what I interpreted it to mean is that the questions on that version of the CoGAT were skewed so as to be answered more correctly by boys than girls.
Is there a trend?: This 75/25 split was not just for one year's data, but a trend over time. What points to me that something is amiss is that neighboring districts that have a similar population of people (and thus I would expect a similar profile of students) have more of an equal number of boys and girls in their gifted math class.
Outside testing: Our district will not use outside testing to determine placement. However, we were able to use my DD10's EXPLORE test results to get her retested on the CoGAT to see if she would now qualify for the gifted math. They did not have the MAP test when my daughter was in 2nd grade and testing for gifted math, so I suspect they gave even more weight to the CoGAT then.
Middle school girls: They also said that they see the trend as girls get older they tend to drop out of the gifted math classes which is probably partially due to peer pressure as someone else stated. That is definitely another problem to tackle, but I think it is separate than the initial identifying in 2nd grade.