Battery Charge doesn't work if starting when EN grounded

What firmware version are you running?

This post by @avtolstoy might be a good starting point for you:

[Edit] - This may not help in your case, but for Solar Recharged Boron's I use the USB connector for the input source.
I get the same results as you when using Vin(Vusb) pin, but charging will resume during/after an EN Pin Shutdown when using the USB connector. I have no idea why :man_facepalming: