Have you tried to use SFTP?
$ ls -la
ls: 0653-345 ./..: Permission denied.
total 112
drwxrwxrwx 15 xxxxxxxx xxxxxxxx 4096 Nov 17 14:37 .
-rw------- 1 xxxxxxxx xxxxxxxx 59 Sep 22 07:58 .Xauthority
-rwx------ 1 xxxxxxxx xxxxxxxx 220 Sep 19 10:33 .profile
-rw------- 1 xxxxxxxx xxxxxxxx 268 Oct 09 09:40 .sh_history
(etc)
The directory contents are listing fine. However, the '..' throws an error, so the whole 'ls -la' command fails when you try to change to a directory. Thus you can't get a directory and file listing for that folder.
The above was done in PuTTY to show that 'ls -la' is actually returning something. WinSCP fails on receipt of the first line instead of parsing the rest of the results.