MySQL Slow Log Missing SQL statements

Hi,

I use pingdom to do basic monitoring of my website and have been noticing a steady march upward for response time. I assume the issue is with my database, so I went to look at my the mysql-slow.log file and see the same three lines repeated with no SQL statements; not exactly helpful.

/usr/sbin/mysqld, Version: 5.1.41-3ubuntu12.6-log ((Ubuntu)). started with:
Tcp port: 3306  Unix socket: /var/run/mysqld/mysqld.sock
Time                 Id Command    Argument

Here is a snippet from the my.cnf file:

log_slow_queries    = /var/log/mysql/mysql-slow.log
long_query_time = 2
log-queries-not-using-indexes

I have just tried changing permissions on the files and directory and restarted mysql with no luck. I still am getting new additions to the mysql-slow.log file, but nothing useful. My current permissions are:

:/var/log/mysql$ ls -al
total 31772
drwxrws--- 2 mysql mysql     4096 Aug 26 06:25 .
drwxr-xr-x 7 root  root      4096 Aug 26 06:25 ..
-rw-rw---- 1 mysql mysql 32193324 Aug 27 02:12 error.log
-rw-rw---- 1 mysql mysql   125493 Aug 27 02:11 mysql-slow.log

Any suggestions for what I am missing?

Thanks, Josh