MySQL 5.1.36 on FreeBSD 7.2 amd64/i386 not honoring wait_timeout

[cruel symbol]

I installed mysql51-server from the ports.

# cd /usr/ports/databases/mysql51-server
# make -D BUILD_OPTIMIZED install clean

Added wait_timeout = 60 to my.cnf and restarted mysql but this is not reflected.

mysql> SHOW VARIABLES LIKE 'wait_%';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| wait_timeout | 28800 |
+---------------+-------+
1 row in set (0.01 sec)


Then I tried setting it from mysql shell
mysql> set global wait_timeout = 30;
mysql> SHOW VARIABLES LIKE 'wait_%';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| wait_timeout | 28800 |
+---------------+-------+
1 row in set (0.01 sec)

MySQL 5.1 notes for FreeBSD says that this problem when using LinuxThreads and should be solved by FreeBSD 5.0. I'm using FreeBSD 7.2 and no LinuxThreads.

Any idea how to get past this.

Thanks