Hi Ulu,
The way the setup works is this:
If the mp_Sites table does not exist it starts with the script:
/Setup/applications/mojoportal-core/SchemaInstallScripts/mssql/2.2.3.4.config
There will always be only 1 script in this folder which is for initial install on an empty db
after that it will run all scripts in correct order from the folder
/Setup/applications/mojoportal-core/SchemaUpgradeScripts/mssql
starting with the next higher script from the one it ran from the SchemaInstallScripts/mssql folder
there are no missing scripts in this folder though some of the script files are empty in which case it will not run the script but will increment the version in mp_SchemaVersion and will still log running the script in mp_SchemaScriptHistory
I would make sure on your machine that there are no extra script files in the SchemaInstallScripts/mssql folder and no missing or extra scripts in the SchemaUpgradeScripts/mssql folder
If the scripts are there I can think of no reason it would run them in incorrect order. It works correctly in my testing. Perhaps you somehow did not get all the files.
Hope it helps,
Joe