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I'm having the same issue with my new Macbook Pro (Mid 2014).
My MBP shows 100 % battery charge , but Coconutbattery just 95%. After this point (MagSafe's led switches to green when status bar shows 100 %) coconut still thinks that the MBP is charging and shows the 100 % after nearly 2 hours. After unplugging my MBP , the status bar indicator stays about 10 Minutes at 100 % while Coconut displays a normal discharge (when coconut shows exactly 95 % charge the status bar starts decreasing, too)
I've noticed the 5 % offset after switching from bootcamp to Mac the first time (Windows forced Sleep Mode at 5 % charge -> after rebooting to Macbook : 5 % offset)
Is there already a solution for this problem? (tried SMC and PRAM reset already)
(Sorry for my bad english)