This problem occurs on both my Vista Business and XP-SP2 system.
When using the Registry Cleaner (RAW mode, aggressive), and when the list of registry items to be deleted is large, and having selected all the items for deletion, Build 446 does not delete all the selected registry keys. It deletes approximately 1/3 of them. To get the rest of the keys, a second scan is required.
As an example, on my XP-SP2 system, the first run of RegCleaner found 1917 keys to be deleted. I selected them all for deletion. The deletion started and cleaned of 378 items. I had to repeat the scan for the remainder of the keys. A third scan showed no keys requiring deletion.
This also occurred earlier on my Vista Business system.