Hi ;
You've done an update by running the script ispcp-setup? If yes, you are mistaken. You must use the ispcp-update script for update.
Edit:
I just test a new installation on Debian Lenny. I encountered no error.
Code:
ispcp:~/ispcp-omega-1.0.3# cd /var/www/ispcp/engine/setup
ispcp:/var/www/ispcp/engine/setup# perl ispcp-setup
    Generating database keys, it may take some time, please wait...
    If it takes to long, please check http://www.isp-control.net/documentation/frequently_asked_questions/what_does_generating_database_keys_it_may_take_some_time_please_wait..._on_setup_mean
        Welcome to ispCP '1.0.3 OMEGA' Setup Dialog.
        This program will set up ispCP OMEGA system on your server.
        Next you are asked to enter a "fully qualified hostname" (FQHN).
        For more infos read http://en.wikipedia.org/wiki/FQDN.
        Please enter a fully qualified hostname. [ispcp.nuxwin.com]: 
        Please enter system network address. [192.168.0.130]: 
        Please enter the domain name where ispCP OMEGA will run on [admin.ispcp.nuxwin.com]: panel.nuxwin.com
        Please enter SQL server host. [localhost]: 
        Please enter system SQL database. [ispcp]: 
        Please enter system SQL user. [root]: 
        Please enter system SQL password. [none]: 
        Please repeat system SQL password: 
        Please enter ispCP ftp SQL user. [vftp]: 
        Please enter ispCP ftp SQL user password. [auto generate]: 
        ispCP ftp SQL user password set to: U,nPrMWDQ.f.PC*+h*H
        Please enter ispCP phpMyAdmin Control user. [pma]: 
        Please enter ispCP phpMyAdmin Control user password. [auto generate]: 
        phpMyAdmin Control user password set to: _^[cS[,8yQzP=!!A$
        Please enter administrator login name. [admin]: 
        Please enter administrator password: 
        Please repeat administrator password: 
        Please enter administrator e-mail address: l.declercq@nuxwin.com
        IP of Secondary DNS. (optional) []: 
        Use MySQL Prefix.
        Possible values: [i]nfront, [b]ehind, [n]one. [none]: 
        FastCGI Version: [f]cgid or fast[c]gi. [fcgid]: 
    Activate AWStats. [no]: 
    Starting Installation...
    Setting GUI Permissions: ....done
    Setting Engine Permissions: .....done
    Congratulations you installed ispCP '1.0.3 OMEGA' successfully!
    Please type http://panel.nuxwin.com in your browser and
    log in with your Administrator Account to use ispCP.
    Setup is now updating rkhunter:
[ Rootkit Hunter version 1.3.2 ]
Checking rkhunter data files...
  Checking file mirrors.dat                                  [ No update ]
  Checking file programs_bad.dat                             [ Updated ]
  Checking file backdoorports.dat                            [ Updated ]
  Checking file suspscan.dat                                 [ Updated ]
  Checking file i18n/cn                                      [ Updated ]
  Checking file i18n/en                                      [ No update ]
  Checking file i18n/zh                                      [ No update ]
  Checking file i18n/zh.utf8                                 [ No update ]
ispcp:/var/www/ispcp/engine/setup#