I'm unable to reproduce this problem with Python 2.5.2 on either Windows
XP or Ubuntu Hardy.

I used a test script (httpd.py, attached). This sets up an HTTP server
which you can use to trigger logging events.

I created a time simulator to allow testing in a timely way. This
monkey-patches the binding for the time module in logging and
logging.handlers to return either the real time or the simulated time.
Once you have started the server (just run the script), you can trigger
a logging event by running

wget -o /dev/null http://localhost:9022/

and you can initiate simulated timing by running

wget -o /dev/null http://localhost:9022/s

The simulated time is set to the next midnight, to facilitate rollover.
I then ran

wget -o /dev/null http://localhost:9022/

three times, then

wget -o /dev/null http://localhost:9022/s

once, then

wget -o /dev/null http://localhost:9022/

again three times. The only files created were:

vinay@zeta-hardy:~$ ls -l  httpd.log*
-rw-r--r-- 1 vinay vinay 192 2009-06-10 16:46 httpd.log
-rw-r--r-- 1 vinay vinay 256 2009-06-10 16:46 httpd.log.2009-06-10

which is as expected, and the contents are:

vinay@zeta-hardy:~$ cat httpd.log.2009-06-10 
2009-06-10 16:46:22,999 pid: 512 DEBUG - OK 2009-06-10 16:46:22
2009-06-10 16:46:23,765 pid: 512 DEBUG - OK 2009-06-10 16:46:23
2009-06-10 16:46:24,406 pid: 512 DEBUG - OK 2009-06-10 16:46:24
2009-06-10 16:46:25,974 pid: 512 DEBUG - OK 2009-06-10 16:46:25

and

vinay@zeta-hardy:~$ cat httpd.log
2009-06-11 00:00:01,260 pid: 512 DEBUG - OK 2009-06-11 00:00:01
2009-06-11 00:00:01,923 pid: 512 DEBUG - OK 2009-06-11 00:00:01
2009-06-11 00:00:02,547 pid: 512 DEBUG - OK 2009-06-11 00:00:02

which is again as expected.

Please try out the test script in your environment and feed back the
results you get.