See this thread for some more tips:
http://www.scalix.com/forums/viewtopic.php?p=51749
It looks like you're trying to install Scalix on a machine that already has a Scalix installation and some of the old stuff is arguing with the new. There's a reason why I asked if you were trying to do a completely new install (ie, you're upgrading your Scalix version and plan to start over with an empty mailstore), or you're trying to upgrade Scalix "around" an existing mailstore. If the latter, you need to follow a specific set of steps.
Note: this is my method; there may be others. However, this has one advantage: I KNOW it works.
1. You'll need a good copy of the existing mailstore (flash disk, DVD, whatever). This is essentially the directory "/var/opt/scalix/??," where "??" is the first and last characters of your hostname. Ex., if your hostname is "mailserver," the directory will be "/var/opt/scalix/ms."
2. Do a completely clean install of CentOS. Wipe the hard drives, start fresh. Make sure you use the same hostname as the original (ex., "mailserver"). Don't change it.
3. Once you're sure that CentOS is running and is happy, install Scalix. Do NOT copy the mailstore yet. This is a new, clean installation. Use the same passwords and config info as you would for the old installation, but this is a new, empty mailstore. Create a couple of dummy users and confirm that you can post emails between them.
4. Once you're sure that the new Scalix is happy, stop all Scalix services, then DELETE the new mailstore (in this example, you'd enter something like "rm -f -r /var/opt/scalix/ms").
5. Copy the old mailstore into that same slot, then run "ompatchom," and recreate the database.
That's the quick and dirty. There are detailed, step by step instructions in this thread:
http://www.scalix.com/forums/viewtopic.php?f=5&t=12182&p=55992#p55992
That particular example came from when we moved our mailstore from one server to the other, but the principle is exactly the same.