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It does not sound like a calibre issue... All calibre does is to copy the ePub file to the Touch, and then let's the Touch do it's processing to add the file to the database.
This sounds like either
a) corrupted database on the Touch (NOT related to calibre)
b) corrupted ePub files (possibly calibre but also could be where ever these files come from)
c) mismatched time between PC and Touch
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