Sounds good (the first part, I mean) 
As for the rest, I’d suggest testing after removeÃng the hub and recharging with the Purism charger, just in case, and see if that gets it to full. Then re-try but open the Power Manager to see what it says about the L5’s charge when you use it. Maybe the hub’s own power is not providing enough for all the devices…?
Before that, thoug, the LEDs, see: https://docs.puri.sm/Librem_5/Troubleshooting/LEDs.html (contact Purism support). Not sure about magenta - maybe it’s a combination of blue (charging + notification/message)?