"However the 6540 record difference is alarming."
that is odd... did you look for repeats in the to list to see if it was looping?
Was that a subset of your database, is it possble the filter wasn't maintained across the submit that initiated the email blast?
"The EmailError (TEXT) field in MySQL filled up as it appears to append all responses collectively. "
That also seems wrong, it should only show the most recent error in the log. I'll have to look into that some more.