The only issue that I ran into with regards to battery is I got an error when I ran 2x18650 in series. The toggle fails to respond and you get some random character across the display. The max input voltage on that chip is only 4.5V. This is why it complained a little. So, putting the batts in parallel fixed this.
Not saying this is your issue, but you might want to check the output voltage on your batts.