As reported for jv16 2007 version 1.7.0.416, the Registry Cleaner will not "remember" items marked as "Never show again". This problem is still occurring on version 1.7.0.420. I am assuming the same problem still exists for the History Cleaner.
The workaround suggested by tullik still works well:
Add item(s) to be ignored to the Registry Cleaner Ignore words tab.
Thanks