The initial value of the variable $counter is set to the highest
checksum_xref.checksum_xref_id found if the table in question is not
empty, or 0 if it is. This causes problems if $counter is only
incremented after each use in the input-file loop:
 - for a non-empty table the parser would attempt to re-use an existing
   value of checksum_xref_id for the first entry read from the input
   file. checksum_xref_id is the primary key of checksum_xref so its
   values have to be unique, therefore "LOAD DATA" silently discards the
   offending row;
 - for an empty table we lose one input row as well but it is the SECOND
   rather than the first one. Reason: 0 is not a valid value for
   auto_increment fields in MySQL, resulting in the first row being
   inserted with the first allowed ID value of 1 - which brings us back
   to the previous scenario when "LOAD DATA" attempts to insert the
   second row.

Incrementing $counter before use ought to address both forms of the
problem.