I had this issue long ago with many DS1307's. I found a Dallas app note that suggests a large negative going spike on the supply rail will corrupt the clock. I verified with a scope that upon power up my supply was indeed going negative by five or ten volts. I put a shottky across the 5 volt line to clamp the negative spike and have not had a re occurrence of the corruption in many years. See the last page of the attached app note.
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