Some servers are case sensitive and will treat two items with the same name typed in different case as two different files. For instance, if you sent a file called TEST.txt to a case sensitive server that already had a file called test.txt, you would not be prompted to overwrite the destination file, instead the server would keep both files. If you connect to such a site in CuteFTP, CuteFTP will treat the files as the same, unless you change settings for the site.
Click on the site in the Site Manager.
(You can skip this step in CuteFTP Home) On the menu bar, choose File > Properties.
Click the Type tab.
In the Server type list choose Unix-compatible.