If you have the latest code and a clean db it should not run that script at all, so this must be an upgrade? or the mp_Sites table is already there so it thinks its an upgrade
On a clean install It should start with:
/Setup/applications/mojoportal-core/SchemaInstallScripts/mssql/2.2.3.4.config
then it should run the ones with higher versions than that from
/Setup/applocations/mojoportal-core/SchemaUpgradeScripts
Hope it helps,
Joe