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Problem using Custom Clean

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We have seen one a couple of similar reports - and the problems cleared themselves without further action from the users.  It seems to be a Windows issue not CCleaner.

A Restart of the computer may clear the issue. ('Restart' not 'Shut down' if it's Windows 10).

It's unsure but it seems to be the new multi-clipboard feature in Windows that may be causing it, even if you are still using the single clipboard.
The multi-clipboard is still being developed/tweaked by Microsoft so it's possible for it to change without warning.

Another issue is if your clipboard is synced and so storing clips in the cloud - CCleaner can't touch those.
CCleaner can clear the local clipboard files stored on your machine, but it can't delete things off Microsofts servers (the cloud).

This explains more about how the multi-clipboard and syncing works, and tells you how to clear clips/history from the MS syncing servers:

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