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Well, this is not exactly true.
What's happening is that Keyboard Maestro's clipboard history “helpfully” removes duplicate entries.
Personally I think this is a terrible feature in that the user has no control over it – nor do I think it's documented in the manual.
The idea that a user would never need duplicate entries in the clipboard history is shortsighted.
My opinion is that the user should be able to either toggle this feature on/off – or that duplicates should always be accepted, but the user could at their discretion remove duplicates from the history.
Of course having both options would also be acceptable.
LaunchBar's clipboard history and Paste.app both play the same game, so this heavy-handedness is not limited to Keyboard Maestro.
So, what's the solution?
I do NOT recommend dictionaries – they are too complicated to mess with for this task.
It depends upon how bad you want to use the feature – I'd just roll my own paste-pop with a Keyboard Maestro variable instead of the KM Clipboard History.
Frustrating... But it is what it is.