I did extensive testing on this when a firmware update came out near the end of may and this issue was first reported. This is not a problem with the batteries, it is how the total capacity is checked and how LiPos degrade over time.
I flew 6 batters after the firmware upgrade (three batteries had been previously flown, 3 batteries never flown, but charged to 100%)
The three batteries flown all exhibit similar behavior, towards the end of the power curve (about 20 to 30%) they had a rapid "discharge indication" that is they went from 20% to 7%
The batteries that had never been flown, did not exhibit this extreme behavior.
I than insured all the batteries were taken down to 5% and charged back to 100%. After this deep cycle all 6 batteries performed as designed for over 10 flights for each battery.
You MUST deep cycle your batteries after a firmware upgrade (to be safe) and after extensive number of flights (20 charge cycles) or if the batteries have not been flown for a significant amount of time (several weeks)