I've seen iRex mention in the past that they've seen a weird scenario where an interrupt from a CF card can interfere with the battery status indicator. I don't remember ever hearing if they solved it in a software update. I guess not if you're running the latest OS.
As far a I know, it doesn't hurt the battery or have any effect on the amount of life you get from a charge, it just makes the battery meter on the screen not work.
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