I'm afraid I don't quite understand what is the problem you are reporting here. If you mean jv16 PowerTools starts and shows Initial Setup again after you have ran the System Cleaner, this is by design and normal. The Initial Setup is run when the program first starts but also when major changes have been made to the system, such as software uninstalled or after a big cleanup with System Cleaner. This is also mentioned in the Initial Setup's message:
"The program is currently running the Initial Setup. This means your system is currently being analyzed to ensure jv16 PowerTools will work optimally on this system. For example, all the installed software in your system are being detected to ensure the System Cleaner does not delete any data relating to them. This is one of the unique safety features of jv16 PowerTools.
No data is sent to anyone and this process must be done usually only this one time. It may have to be ran again after updating this software, or if you make major changes to your computer. This process will take 1-5 minutes to complete."