Untill now I didn't add anything to the slave server, so no records added, sites or email, users etc. So this server is clean.
Ok, this explains the problem. The database is smaller as the installer expects it to be as it is empty.
You have to edit the update.php script and set the size limit to a lower vale. Edit line 152 and chnage it from:
if(filesize('existing_db.sql') < 30000) .....
if(filesize('existing_db.sql') < 20000) .......
and then run the update.php script again.