entries not deleted by hijackthis

Hi guys,
i got an odd trouble with my Pc. It's a brand new HP Intel i5 4gb ram and with win 7 64b. After a couple of months of frequent use (although I use to switch it off every night) I wanted to clean up my registry with cc cleaner and hijackthis. I did it and the performance improved but I realized that hijack was not able to delete a lot of empty entries.
Well, it's not an actual problem -if the items are clean there shouldn't be any problem, right?- but how is it possibile? It's pretty annoying to see a long log full with empty entries when you don't have all that stuff on your PC.
Thanks
Bye