I would bet the iLiad can't detect via software if it's plugged in. The LED could be controlled by the charging electronics as well. So this would be mainly a hardware design flaw.
IIRC some people had problems with a wrong battery level on a running iLiad, and it turned out it was due to the battery.o kernel module provided by iLiad. Your problem will probably be related to that rather than a memory effect of your battery.
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Once we get the freedom of the developers' kit, we can solve our own problems, but until then we're completely at their mercy, and the bug can block us from installing the developers' kit.
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Unfortunately the upgrade mechanism is outside the user-accessable memory and thus can't be upgraded by the community in an easy manner. At least chances are great that you'll brick your iLiad if you try to alter it.