slow_query_log missing queries

mysql> SELECT VERSION();
+-----------------+
| VERSION() |
+-----------------+
| 5.6.32-78.0-log |
+-----------------+
1 row in set (0.00 sec)

Current settings

| log_slow_admin_statements | OFF |
| log_slow_filter | |
| log_slow_rate_limit | 1 |
| log_slow_rate_type | session |
| log_slow_slave_statements | ON |
| log_slow_sp_statements | ON |
| log_slow_verbosity | |
| log_throttle_queries_not_using_indexes | 0 |

mysql> show variables like 'min%';
+------------------------+-------+
| Variable_name | Value |
+------------------------+-------+
| min_examined_row_limit | 0 |
+------------------------+-------+

Thank you for the report.

You have option

| log_slow_admin_statements | OFF |

Could you please turn it ON, try again and if issue still repeatable provide example of queries which were not logged?

SET GLOBAL log_output='TABLE';
SET GLOBAL slow_query_log=0;
SET GLOBAL general_log=0;
TRUNCATE TABLE mysql.slow_log;
TRUNCATE TABLE mysql.general_log;
SET GLOBAL long_query_time=0;
SET GLOBAL log_slow_rate_type = 'query';
SET GLOBAL slow_query_log=1;
SET GLOBAL general_log=1;
SET GLOBAL log_slow_admin_statements = 1;
SELECT SLEEP(120);
SET GLOBAL slow_query_log=0;
SET GLOBAL general_log=0;

SELECT (
SELECT COUNT(*) FROM slow_log WHERE lcase(sql_text) LIKE '%update%'
) slow,
(
SELECT COUNT(*) FROM general_log WHERE lcase(argument) LIKE '%update%'
) general;
mysql> SELECT (
    -> SELECT COUNT(*) FROM slow_log WHERE lcase(sql_text) LIKE '%update%'
    -> ) slow,
    -> (
    -> SELECT COUNT(*) FROM general_log WHERE lcase(argument) LIKE '%update%'
    -> ) general;
+------+---------+
| slow | general |
+------+---------+
| 645 | 923 |
+------+---------+
1 row in set (0.88 sec)

Queries missing are all of the same format, very simple primary key single row updates
e.g.
UPDATE tevoc SET `ev_oc_id` = '60750331',`ev_mkt_id` = '9675871',...... WHERE ev_oc_id = '60750331'

Percona now uses JIRA for bug reports so this bug report is migrated to: https://jira.percona.com/browse/PS-3735