I had this happen to me on stock as well the first day I owned the phone. Left it on the charger all night and on less than ten minutes of use the battery showed 1%. Charged back to full and haven't seen it again. I think server people have experienced this bug.
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Nexus 4 running Stable CM 10.1
GSM Galaxy Nexus
HTC One S
HTC MyTouch 4g Slide