I Googled a bit and found out that I had to re-run the Repository Creation Utility, as apparently there is an extra environment variable to set before you run this. I fixed it as follows:
- Open a dos-box in the ..\rcuHome\bin folder
- Enter: set rcu_jdbc_trim_blocks=true
- Run rcu.bat
- Drop the existing repository
- Recreate a new one
- All invalid objects disappeared!
set DEFAULT_MEM_ARGS=-Xms512m -Xmx768m