Assuming your speed controls have built in BEC circuits, try disabling one BEC by removing the positive pin from one of the ESC connectors. Use the tip of an Xacto knife to lift up the little plastic retaining clip, and pull out the pin. The positive is in the middle. Cover the exposed pin with heat shrink so it doesn't short to anything. Alternately, you could remove (or even cut) the positive wire on one leg of the Y harness where one of the ESC's plug in. Having potentially slightly different BEC voltages both feeding into the Y-harness can make the ESC's unhappy, in my experience.
Just out of curiosity, are you simply plugging one lipo into each ESC, or are you paralleling the packs and feeding both ESC's the same power?