I'm not sure how to test this.  The problem isn't reflected in that select query.  Whenever ptc finds an error, it exits with a non-zero exit code.  But if I immediately query the replicate table, no differences are present.  Here's the latest:

1. Ran the following in a while loop:
do
   /sso/sfw/percona/bin/pt-table-checksum --user=root --password=blah --chunk-size-limit=50.0 --replicate-check --recursion-method=DSN=D=percona,t=dsns_ssodb03 --databases=vsp_jira_current --tables=customfieldoption --no-check-replication-filters --replicate=percona.checksums_ssodb03
   if [ "$?" != "0" ]; then
      break;
   fi
done

2. Loop ran 9 times with a 0 exit code, and on the 10th try, it exited with the following output:
            TS ERRORS  DIFFS     ROWS  CHUNKS SKIPPED    TIME TABLE
12-12T13:51:14      0      1     1734       1       0   0.018 vsp_jira_current.customfieldoption

So it thinks there is a difference in vsp_jira_current.customfieldoption.

3. Examine replicate table on master:
mysql> select * from checksums_ssodb03 where tbl='customfieldoption';
+------------------+-------------------+-------+------------+-------------+----------------+----------------+----------+----------+------------+------------+---------------------+
| db               | tbl               | chunk | chunk_time | chunk_index | lower_boundary | upper_boundary | this_crc | this_cnt | master_crc | master_cnt | ts                  |
+------------------+-------------------+-------+------------+-------------+----------------+----------------+----------+----------+------------+------------+---------------------+
| vsp_jira_current | customfieldoption |     1 |   0.006716 | NULL        | NULL           | NULL           | a83c0464 |     1734 | a83c0464   |       1734 | 2012-12-12 13:51:14 |
+------------------+-------------------+-------+------------+-------------+----------------+----------------+----------+----------+------------+------------+---------------------+
1 row in set (0.00 sec)
mysql> SELECT CONCAT(db, '.', tbl) AS `table`, chunk, chunk_index, lower_boundary, upper_boundary, COALESCE(this_cnt-master_cnt, 0) AS cnt_diff, COALESCE(this_crc <> master_crc OR ISNULL(master_crc) <> ISNULL(this_crc), 0) AS crc_diff, this_cnt, master_cnt, this_crc, master_crc FROM `percona`.`checksums_ssodb03` WHERE (master_cnt <> this_cnt OR master_crc <> this_crc OR ISNULL(master_crc) <> ISNULL(this_crc)) AND (db='vsp_jira_current' AND tbl='customfieldoption');
Empty set (0.00 sec)

4. Examine replicate on slave:
mysql> select * from checksums_ssodb03 where tbl='customfieldoption';
+------------------+-------------------+-------+------------+-------------+----------------+----------------+----------+----------+------------+------------+---------------------+
| db               | tbl               | chunk | chunk_time | chunk_index | lower_boundary | upper_boundary | this_crc | this_cnt | master_crc | master_cnt | ts                  |
+------------------+-------------------+-------+------------+-------------+----------------+----------------+----------+----------+------------+------------+---------------------+
| vsp_jira_current | customfieldoption |     1 |   0.006716 | NULL        | NULL           | NULL           | a83c0464 |     1734 | a83c0464   |       1734 | 2012-12-12 13:51:14 |
+------------------+-------------------+-------+------------+-------------+----------------+----------------+----------+----------+------------+------------+---------------------+
1 row in set (0.00 sec)

mysql> SELECT CONCAT(db, '.', tbl) AS `table`, chunk, chunk_index, lower_boundary, upper_boundary, COALESCE(this_cnt-master_cnt, 0) AS cnt_diff, COALESCE(this_crc <> master_crc OR ISNULL(master_crc) <> ISNULL(this_crc), 0) AS crc_diff, this_cnt, master_cnt, this_crc, master_crc FROM `percona`.`checksums_ssodb03` WHERE (master_cnt <> this_cnt OR master_crc <> this_crc OR ISNULL(master_crc) <> ISNULL(this_crc)) AND (db='vsp_jira_current' AND tbl='customfieldoption');
Empty set (0.00 sec)

5. So there aren't any differences in the replicate table between the master and slave.  The only indication there is a difference is in pt-table-checksum's output and its exit code.