The Cleaning engine of v1.4.x is diffrent then the 2005 version.
The 2005 can find more faulty entries, and it is also much safer. It will exclude more entries which are know to cause problems.
Also, PowerTools has an option to update the Cleaner engine, which will add or remove entries which are faulty.
The Software Manager lists all software entries found in the regsitry.
These entries can't always be cleaned automaticly, becouse it can't always see if the software is still installed or not. That is what the Software Manager is for :).