This is a quite rare but major problem. Occasionally when you get corrupt data on your memory card the Media Linker will only show a single block of data (usually the system data) and the EMS software shows nothing, hanging after reading the card. Normally the corrupt data does not affect the operation of the Linker software but sometimes it can. If this happens then the only thing you can do is format the card, but first backup the data on the card using either the Xport/SharkPort or by copying it to another card.
Be sure to make regular backups of your saves.
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EMS Memory Adapter FAQ