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Play in the connector?
When you plug in the retractable cable, is there more play (looseness) in the connection vs. the stock cable? You said this happened over time, which suggests the connector inside the Nook has loosened. There are typically a couple of tabs on a USB female connector to help maintain proper alignment of the connectors.
The bad news: if this is the issue, I don't know of how to fix it without opening the Nook to (slightly) bend the tabs.
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