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No, you are misunderstanding how the discharge function works.Sounds like you may have just dodged the bullet on the firmware bug. Apparently the automatic self-discharge is very slow so that it does not generate excessive heat. I'd bet that if you had waited longer your batteries would have discharged until they were dead.
I would recommend keeping an eye on them anyway to be sure they were not damaged by over discharging.
The self discharge only takes the pack down to circa 3.86v per cell after a pre determined time (1-10 days set by the user).
If left unattended they DO NOT continue to discharge - they go into a hibernation state of extremely low quiescent current and must be 'woken up' from this stage in order to accept a charge again. What you experienced by the sound of it is NOT an over discharge condition but a failure to wake from hibernate.