Firstly, thank you for your response.
Even when I left the "clones only" button checked, it does not show the clones (nothing happens). No matter if I search inside boxes, savedata or backups. If I remember correctly, earlier versions of PKHeX would have shown the clones, if only the "clones only" was checked (minus the legal and illegal). I might be wrong but searching for clones only it appears to be hiding the clones, not making them visible on the search results.
I have tried with search inside boxes, savedata or backups and checked and unchecked all possible combinations.
Clones do not appear when I check the "clones only", just the legal and illegal pokemon. There is no way (of what I have tried so far) to make only the clones appear on the search results.
Checking the clones only button "hides" the clones from the search results, unchecking the "clones only" makes them appear in the search results, along with the legal and illegal pokemon.
If it works as intended, I am sorry for insisting on that issue