Isso foi levantado nos fóruns do FileZilla, veja este tópico .
In version 2 there was a checkbox on the File Transfer Setting page: "Display all file revisions on VMS servers". When you unchecked that, only one file revision would be shown without the trailing semicolon and version number and those would not be included in the local file name either.
Você pode encontrar links de download da versão 2 aqui .