I had simmilar issue using VIN. I can't believe Pycom doesn't provide any schematic for these expansion boards, or atleast proper descriptions on how they can be used. I was also under the impression that VIN can be used as an input, instead of using the USB. There are NO WARNINGS anywhere that you should not be using VIN as an input, while using a battery as a backup. Luckily my house didn't burn down as I soon enough figured out that VIN and the Battery + seem to be linked together...
I'm new to Pycom's hardware - and thus far really disappointed in the lack of usefull (and up to date) documentation