It's still not working. The ISPConfig server.sh script is not removing the lock file after it runs unless I run it from a command prompt.
If I remove the file manually, it will run one time from the panel and not again. I keep getting "There is already an instance of server.php running. Exiting." in the System Log every minute (which means cron is running the script every minute like it's supposed to). This is happening on both of my servers. They are both running Squeeze and are up to date. This happened right after the upgrade to ISPConfig 126.96.36.199 but I also did some other updates as well on both servers (the usual apt-get update, apt-get upgrade) at the same time. My systems were working perfectly up to then.