What if they went "The Prestige" on us? If you haven't seen The Prestige, spoilers follow:
So in that movie Bales character is revealed to have an identical twin and they work together taking turns on who is the main guy and who's disguised. The other twin falls in love and things and things.
So the two Jays, Zolomon and E-2 Jay are both in on it trying to steal Barrys speed, but the other Jay falls in love with Caitlin, things get complicated and the other Jay murders the other. Make any sense to anyone? At first they take turns on being Zoom and being Jay. That would explain why Jay didnt help when Star Labs was attacked by the earth quake dude. He was the more evil one and just didn't care.