Doesn't make sense. No way the multiair actuators would get current to have the intake valves stay open whilst at the same time a spark is fired. Even if the mechanical timing was off. The wrong timing might cause a spark with the exhaust valves still open, as the timing for the exhaust valves is mechanical. But for the intake valves to stay open because of the multiair the actuators would need to receive current at the exact moment of the spark.
Did you check for bent intake valves? If they're bent they might not slide back to the fully closed position, so they stay permanently open.