I had this trouble once and it turned out to be a bad Sevcon controller near the battery. After We replaced the controller and ran it through a few cycles it worked correctly. It is expensive but you can also swap it out for a generic booster if you are comfortable with wiring. 36V 48V to 12V 20A 240W DC DC Step Down Converter Voltage Regulator.
This may or may not work, but it is something to try.