When you have a query that returns more than 1000 rows, SQLyog will auto-limit the result set to 1000 rows.
Query execution stats are shown for the limited query at the bottom of the SQlyog Window (Exec, Total).
However, when you clear the “Limit rows” checkbox, it re-runs the query without the limit, but does not update the execution time stats.
If you then re-execute the same query, the execution stats will be updated. However, if it’s a slow query, this is inconvenient. Also, the execution time may be quicker than the first execution if pages are now cached in memory on the server.