OK, thanks.
WinSCP definitely cannot copy with this.
To me it looks at least like an inconsistency, if not a bug, when root has path /, but when entering subdirectory, a leading slash disappears.

Hi,
Thanks for the reply.
This is the session log for /storage/emulated:

Session LOG:
=================================================
--------------------------------------------------------------------------
WinSCP Version 5.5.4 (Build 4433) (OS 6.1.7601 Service Pack 1 - Windows 7 Home Premium)
Configuration: HKEY_CURRENT_USER\Software\Martin Prikryl\WinSCP 2\
Local account: OPHER-TOSH\Opher
Working directory: C:\Program Files (x86)\WinSCP
Process ID: 17516
Command-line: "C:\Program Files (x86)\WinSCP\WinSCP.exe"
Time zone: Current: GMT+3, Standard: GMT+2 (שעון רגיל ירושלים), DST: GMT+3 (שעון קיץ ירושלים), DST Start: 28/03/2014, DST End: 26/10/2014
Login time: יום חמישי 10 יולי 2014 23:31:30
--------------------------------------------------------------------------
Session name: p4sKg11j@127.0.0.1 (Modified site)
Host name: 127.0.0.1 (Port: 18890)
User name: p4sKg11j (Password: Yes, Key file: No)
Tunnel: No
Transfer Protocol: FTP
Ping type: C, Ping interval: 30 sec; Timeout: 15 sec
Proxy: none
Send buffer: 262144
UTF: 2
FTP: FTPS: None; Passive: Yes [Force IP: A]; MLSD: A [List all: A]
Local directory: default, Remote directory: /storage/emulated, Update: No, Cache: Yes
Cache directory changes: Yes, Permanent: No
DST mode: 1; Timezone offset: 0h 0m
--------------------------------------------------------------------------
Connecting to 127.0.0.1:18890 ...
Connected with 127.0.0.1:18890. Waiting for welcome message...
220 SwiFTP 3.26.0 ready
USER p4sKg11j
331 Send password
PASS ********
230 Access granted
SYST
215 UNIX Type: L8
FEAT
211-Features supported
UTF8
211 End
OPTS UTF8 ON
502 Unrecognized option
Connected
--------------------------------------------------------------------------
Using FTP protocol.
Doing startup conversation with host.
PWD
257 "/"
Changing directory to "/storage/emulated".
CWD /storage/emulated
250 CWD successful
Getting current directory name.
PWD
257 "storage/emulated"
Retrieving directory listing...
CWD /storage/emulated/storage/emulated/
550 Can't CWD to invalid directory
Could not retrieve directory listing
LIST with -a failed, will try pure LIST
Retrieving directory listing...
CWD /storage/emulated/storage/emulated/
550 Can't CWD to invalid directory
Could not retrieve directory listing
(ECommand) Error listing directory 'storage/emulated'.
Could not retrieve directory listing
Can't CWD to invalid directory
Startup conversation with host finished.

WinSCP gets confused by absence of leading slash in response to PWD command.

Can you test what is a response like when you are two folders deep?

I'm running SnapPea to connect my android phone.
It is using SwiFTP as an ftp server to expose the Android file system.

When browsing with Windows Explorer it all works as expected,
But with WinSCP I can't CD into any directory (see log below).
I've noticed two forum topics on this issue from 2012 that seem to not have been resolved.

Session LOG:
=================================================
--------------------------------------------------------------------------
WinSCP Version 5.5.4 (Build 4433) (OS 6.1.7601 Service Pack 1 - Windows 7 Home Premium)
Configuration: HKEY_CURRENT_USER\Software\Martin Prikryl\WinSCP 2\
Local account: OPHER-TOSH\Opher
Working directory: C:\Program Files (x86)\WinSCP
Process ID: 27884
Command-line: "C:\Program Files (x86)\WinSCP\WinSCP.exe"
Time zone: Current: GMT+3, Standard: GMT+2 (שעון רגיל ירושלים), DST: GMT+3 (שעון קיץ ירושלים), DST Start: 28/03/2014, DST End: 26/10/2014
Login time: שבת 28 יוני 2014 02:11:01
--------------------------------------------------------------------------
Session name: dj3k9af3@127.0.0.1 (Modified site)
Host name: 127.0.0.1 (Port: 18872)
User name: dj3k9af3 (Password: Yes, Key file: No)
Tunnel: No
Transfer Protocol: FTP
Ping type: C, Ping interval: 30 sec; Timeout: 15 sec
Proxy: none
Send buffer: 262144
UTF: 2
FTP: FTPS: None; Passive: Yes [Force IP: A]; MLSD: A [List all: A]
Local directory: default, Remote directory: /storage, Update: No, Cache: Yes
Cache directory changes: Yes, Permanent: No
DST mode: 1; Timezone offset: 0h 0m
--------------------------------------------------------------------------
Connecting to 127.0.0.1:18872 ...
Connected with 127.0.0.1:18872. Waiting for welcome message...
220 SwiFTP 3.26.0 ready
USER dj3k9af3
331 Send password
PASS ********
230 Access granted
SYST
215 UNIX Type: L8
FEAT
211-Features supported
UTF8
211 End
OPTS UTF8 ON
502 Unrecognized option
Connected
--------------------------------------------------------------------------
Using FTP protocol.
Doing startup conversation with host.
PWD
257 "/"
Changing directory to "/storage".
CWD /storage
250 CWD successful
Getting current directory name.
PWD
257 "storage"
Retrieving directory listing...
CWD /storage/storage/
550 Can't CWD to invalid directory
Could not retrieve directory listing
LIST with -a failed, will try pure LIST
Retrieving directory listing...
CWD /storage/storage/
550 Can't CWD to invalid directory
Could not retrieve directory listing
(ECommand) Error listing directory 'storage'.
Could not retrieve directory listing
Can't CWD to invalid directory
Startup conversation with host finished.