Notice how on every other day the telporters seem to be used they have negative side effects, turning the user into a zombie. The day of an eclipse, the teleporters WORK and do not cause zombification....and there are dates circled on a calender that are about a lunar cycle...so if the scientists were paying attention to the moon, obviously it has an effect. I say the eclipse allows the telporters to complete matter transfers without as many adverse side effects, why else would group 935 care about the moon so much?
On a side note, this could also be messing with the clock somehow...treyarch says the big secret is right in front of us well whats more in our face then the obviously emphasized moon?