Several times in the past I have found duplicate keys in the registry. They are differentiated by a .1 extension. In one case they came about after a dual boot Windows install. I manually deleted the second copy of Windows and removed its entry from the boot menu. I suspect duplicate keys also can appear when an app is manually deleted.
The CCleaner Registry Cleaner does not recognize these duplicate keys. It would be nice if it could remove them when it cannot find the corresponding folder.
if the reg key has a .1 at the end, then it will not be flagged as a duplicate, since it's hive entry is, after all, unique.
a more concerning question is "what put it there?". some process wanted to store the same name but found one already there so whacked on the .1
I suspect you are right in the theory it has had something to do with some sort of manual usage of the registry. (rogue software, human error, over-zealous cleanup tool etc).
since CC wouldn't recognise them as 'duplicates' and if they were orphaned registry entries, then they should still be cleaned by CC.
what were the entries in question? did you do some investigating to discover if the corresponding folders were there?