By supposing that you are using reliable (providing USB-DCP/BC1.2 5V/1.5A charging protocol) power supply, point that I forgot to mention in my here related post is that you should want to follow this post of mine, here please do not skip step you mentioned here, by having your Librem 5 powered off, to wait until indicator red LED light off (trickle charge stops):
P.S. If above doesn’t help directly you might want to take BPP-L503 battery out during usage of Librem 5 (powered on and connected to the reliable power supply), and put same Librem 5 battery back after few seconds (and repeat here made up procedure, getting there where you want to have energy-full value properly set by “forcing” or rather waiting to get red LED light off in both charging scenarios, with Librem 5 on and with Librem 5 off).