The v1.1 release still has a bug with folder names containing "." characters.
Example of the problem:
PC "XXX\Soul.Calibur.4.PS3\GameFiles" ---> FTP transfer ---> "XXX\GameFiles"
Notice that it will transfer the files inside the "Soul.Calibur.4.PS3" folder, but when it saves the files on the PS3 it will dump all the files on the HDD without that folder directory there.
Just make a folder name containing "." characters, drop a few test files in it, then transfer the entire folder over the FTP app and you will see exactly what I mean.