CCleaner Issue Scanner seems to be unable to delete hidden Start Menu shortcut (.lnk) files. The issue is completely reproducible and definitely tied to the "Hidden" flag in the Windows file system (in that removing it always resolves the issue).

CCleaner v1.36.430
MS Windows XP SP2
Intel Pentium D CPU 3.00GHz, 1.0GB RAM, ATI FireGL V3100

Welcome to the forums
So your sure it's not spyware or something causing this?
I'd post a HJT log just in case
There's a seperate forum for that.
-aaron

Thank you, Aaron. I think you may have misunderstood my question. Let me clarify to be sure: I'm hiding the files in the Start Menu. I do that sometimes with shortcuts that I don't want to appear all the time but that I still want access to in a pinch. So I'm not blaming that on CCleaner. I hid the files, and I meant to hide them. It's just that those files, being hidden, CCleaner is for some reason unable to delete when it wants to. Is that clearer?

Yes, clear now.
It may be a security issue.
A lot of Windows files are hidden and Ccleaner may be set to not delete hidden files, or not even search them.
Files aren't stored in the start menu, thos are just shortcuts.
Do you know what it WOULD be cleaning if they weren't hidden?

Well, shortcuts actually are files, and they're what CCleaner is trying to remove in my case. Here, I'll brake the issue down precisely--it comes about like this:

1. I install some software. I don't use it much, so I hide the shortcut in my Start Menu for the rare occasion I really need it.
2. Later I decide to just uninstall it, but--maybe I rearranged the Start Menu, maybe there's an oversight in the uninstaller--it doesn't get the shortcut.
3. I run the CCleaner Issue Scanner and the File Integrity > Start Menu Shortcuts scan identifies the problem "Missing Shortcut reference," data "C:\Documents and Settings\All Users\Start Menu\Programs\Example.lnk. Solution: Delete the shortcut file."
4. Attempting to fix the issue results in "Error fixing file issue (1). File: [C:\Documents and Settings\All Users\Start Menu\Programs\Example.lnk] File not found."

Now, if I change the Hidden attribute on that file, CCleaner finds and deletes it just fine. So the problem, apparently, is that CCleaner scans hidden files but fails for some reason to manipulate them. Knowing, thus, precisely where the bug resides, I could imagine it being fairly easy to fix.