I honestly think that the fault will lie with one or more of the 16 connector pins that come away from the connector that the MicroSD reader seats into..
I experienced an almost exact issue to you, tried to fix it in exactly the same way but came to the conclusion it was due to one of those pins having a broken connector. Whether this happened prior to replacing the reader or during, the end result stands. Those pins seem to be susceptible to damage if the MicroSD reader connector is disconnected with too much force... Doh.. :/