MySQL’s “slow query” log: strange “Query_time”

I need some help understanding what's going on with my "slow query" log in MySQL. I have set

 set global long_query_time=3

and yet this is what I see in the slow query log:

# Time: 120723  9:04:38
# User@Host: root[root] @  [111.111.111.205]
# Query_time: 0.017508  Lock_time: 0.000111 Rows_sent: 2884  Rows_examined: 9132
SET timestamp=1343027078;
SELECT [...]
# User@Host: root[root] @  [111.111.111.202]
# Query_time: 0.030282  Lock_time: 0.000102 Rows_sent: 0  Rows_examined: 12323
SET timestamp=1343027078;
SELECT [...]
# Time: 120723  9:04:41
# User@Host: root[root] @  [111.111.111.202]
# Query_time: 0.004416  Lock_time: 0.000104 Rows_sent: 18  Rows_examined: 6266
SET timestamp=1343027081;
SELECT [...]
# User@Host: root[root] @ hostname [111.111.111.199]
# Query_time: 0.029399  Lock_time: 0.000116 Rows_sent: 0  Rows_examined: 12323
SET timestamp=1343027088;
SELECT [...]
# Time: 120723  9:04:53
# User@Host: root[root] @  [111.111.111.201]
# Query_time: 0.004470  Lock_time: 0.000080 Rows_sent: 0  Rows_examined: 6248
SET timestamp=1343027093;
SELECT [...]
# Time: 120723  9:04:55
# User@Host: root[root] @  [111.111.111.198]
# Query_time: 0.042627  Lock_time: 0.000087 Rows_sent: 0  Rows_examined: 0
use [...];
SET timestamp=1343027095;
UPDATE [...]
# User@Host: root[root] @  [111.111.111.198]
# Query_time: 0.029115  Lock_time: 0.000124 Rows_sent: 0  Rows_examined: 0

where the time in Query_time is significantly lower than my prevously specified 3 seconds. Why's that? Where is the missing time?

MySQL 5.1.41, Ubuntu 10.04