I just put mine in sleep mode with auto rcm installed and then dock it. Stays at 100%.
yeahh, sleep mode is not a problem, only power off while using AutoRCM without having a payload to manage the power off request.
like mattytrog said, you need to insert your dongle when you power off in order let the payload do the proper shutdown of the console. at least, if the payload you are using is compatible with real power off commands, like Hekate. I don't know about SX OS, or other paylods.
One thing which has never been said here : if you plug your console into the dock AFTER shutdown, it will silently boot the console, and you'll be back to RCM!
So, do not plug any powered USB device after a full shutdown or it'll power ON and get stuck in RCM with battery drainage.
If you want to put your console to charge while being OFF, you need to plug it into the dock (or charge cable) before doing the payload's proper shutdown. This way, it will stay off but still charge.
I didn't test charging in the dock before real shutdown as I need to put my payload on USB, but it's what I've read. internal modchip might be easier to do both payload inject and charge in power off state.
Another way is to not use the "Auto HOS shutdown" feature to auto-shutdown at hekate launch, once in hekate unplug your USB and plug the console in the dock and then choose shutdown option with Vol/power button.