I went through the upgrade process successfully but the version number did not increment from 2.2.11 to 2.2.12 (the alert flag did disappear). I am using TimeTrex Business Edition On-Site running on a Ubuntu 8.04 server. Although I used the .zip for my installation, I used a .bin for the upgrade.
You can't mix and match installation methods. If you used the .ZIP file originally, using the automated installer isn't recommend as an upgrade. It simply won't work.
If you want to do a fresh install, that is fine though.