I have exactly the same issue. I use Xerox WC7535 to transfer scanned doc to FTP via Filezilla.
Filezilla user (name: skaner) has full permissions and also this user has all permissions to directory in Windows.
When scanning only 2 folders are created - Month - 01 and subfolder Day - 22....and this subfolder is empty. No pdf file.
I think xerox setup should be OK. SYSTEM authentication option. It's only IP of server, username and password. Default Repository Document Path - left empty (because path is already configured in filezilla on user)
(000002)22.1.2015. 9:44:53 - (not logged in) (10.50.2.2)> Connected on port 21, sending welcome message... (000002)22.1.2015. 9:44:53 - (not logged in) (10.50.2.2)> 220-FileZilla Server version 0.9.46 beta (000002)22.1.2015. 9:44:53 - (not logged in) (10.50.2.2)> 220-written by Tim Kosse (tim.kosse@filezilla-project.org) (000002)22.1.2015. 9:44:53 - (not logged in) (10.50.2.2)> 220 Please visit http://sourceforge.net/projects/filezilla/ (000002)22.1.2015. 9:44:53 - (not logged in) (10.50.2.2)> USER skaner (000002)22.1.2015. 9:44:53 - (not logged in) (10.50.2.2)> 331 Password required for skaner (000002)22.1.2015. 9:44:53 - (not logged in) (10.50.2.2)> PASS ****** (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 230 Logged on (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> SYST (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 215 UNIX emulated by FileZilla (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> PASV (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 227 Entering Passive Mode (10,50,1,1,220,56) (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> TYPE A (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 200 Type set to A (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> LIST ./. (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 150 Opening data channel for directory listing of "/" (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 226 Successfully transferred "/" (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> MKD /xcse6094 (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 257 "/xcse6094" created successfully (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> MKD /XCSE6094 (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 550 Directory already exists (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> RMD /xcse6094 (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 250 Directory deleted successfully (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> CWD . (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 250 CWD successful. "/" is current directory. (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> PASV (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 227 Entering Passive Mode (10,50,1,1,220,57) (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> TYPE I (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 200 Type set to I (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> RETR 01/22/15_09:55:28_20150122095523.LCK/LOCKINFO.DAT (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 550 File not found (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> MKD 01/22/15_09:55:28_20150122095523.LCK (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 450 Internal error creating the directory. (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> QUIT (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> 221 Goodbye (000002)22.1.2015. 9:44:53 - skaner (10.50.2.2)> disconnected.