There are actually 2 flavors to the same bug (it should be maybe 2 bugs):
1. in non-flaten mode, if the uploaded file path is - for example - dir1/dir2/dir3/file.zip then it creates those folders in the FTP server: dir2, dir3, dir1/dir2/dir3 (where it puts the file). The creation of dir2 and dir3 is wrong!
2. in flaten and non-flaten modes, if the target folder has - for example - the format dir1/dir2/dir3, the created folders in the FTP server are: dir1, dir2 and dir3 while it should create only a structure of dir1/dir2/dir3 and puts it there