It looks to me like you're powering half the motor phases from the Arduino +5, and half from the battery. For a motor that draws one amp, the only connection from the Arduino 5V supply should be VCC1 (16). What happened to the 10k resistor used between that and the ENABLE pins (1 and 9); and there's a return via your diodes connected to the Arduino +5 rail as well.
Your 3.3 ohm resistors are too small. If they're going to carry 1A, they need to be at least 3.3W resistors!