I can't think of any reason why SuperDuper! would only recognize one of the two flash drives. Perhaps it's prompting for the first one because those settings are saved automatically... you need to cancel and insert the 2nd drive (which has to be formatted for HFS+). Try naming both differently to ensure you have the proper drive inserted... this should work fine (we don't even know it's a flash drive).
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--Dave Nanian
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