I guess you have added tables or modified tables in the ispconfig database? Then thats the reason for the problem as it is not supported to modify the table structure manually. If you did modify the tables, you can not install ispconfig updates anymore.
Regarding the configuration changes, thats intended as the updater has to reconfigure the system config to match the requirements of the new version. If you dont want that and modify all config files manually, just choose "no" when the installer asks you if the services shall be reconfigured.