With the batteries I got now I am running a minute each way. But with little batteries its harder to go longer. You gotta switch fast like 10 hertz or so. And depending on the motor you can burn up some energy.
But if your battery are not taking to the proccess you can have problem to.
Get a good charger for them and charge them while they are switching. Then discharge them while switching. Take note on how long it running down and see it if it improves.
I did a 9v battery one once but it didn't work for long time at all so smaller batteries may be hard to handle.