I'm experiencing an issue with making the upgrade from 8.5 to 9.0, hoping that someone can offer some assistance. I have done the uninstall of 8.5 and installed 9.0. The server has been rebooted and all the services are started. The Management Console gives error message "Error occured while initializing the database. This database is pre 9.00 database. Please use Publisher upgrade tool", then the Publisher Upgrade Tool gives error "Upgrade from Publisher Standard Edition is not supported". The QVS reference manual does not give any indication as to what to do when you do not have the full version of Publisher, so I am stuck. What am I supposed to do??
I found out that removing (by for example renaming) the folder C:\Documents and Settings\All Users\Application Data\QlikTech\Publisher\CommandCenter and then restarting Publisher Command Centre gets the job done. You will loose all your reload tasks but this at least gets you past the problem of not being able to upgrade the database.
I had the same situation last week. I had to uninstall previous version, delete all the QlikView folders under program folders and shared folders, and do a new installation. All worked fine then. Hope this helps.