This issue has been resolved already. The fix will be included into the next release.

juhehe wrote:

Perhaps the problem is that the server is having trouble deleting the current working directory. Is "cd .." or "cd ~" a good solution to do before the RMD command?

That's quite probable. I'll fix this in the next version.

WinSCP 4.0.5 using FTP on "ProFTPD 1.3.1rc2 Server",
when deleting directory (here it's named test):

Error
Error deleting file 'test'.
"/home/j/u/junonot/cgi-bin/test/: Invalid argument"

Move operation encounters the same problem: it moves the files succesfully but fails to remove any directory.

Using another ftp client "rmdir test" deleted the 'test' directory just fine.
It was "chmod 711".
Creating a directory using WinSCP405 works fine.

Perhaps the problem is that the server is having trouble deleting the current working directory. Is "cd .." or "cd ~" a good solution to do before the RMD command?
Or is the slash too much at the end of the parameter.
Hopefully I did include enough of the log to be useful:

Session upkeep
Deleting file "test".
Retrieving directory listing...
CWD /home/j/u/junonot/cgi-bin/test/
250 CWD command successful
PWD
257 "/home/j/u/junonot/cgi-bin/test" is the current directory
TYPE A
200 Type set to A
PORT 192,168,0,187,12,6
200 PORT command successful
LIST -a
150 Opening ASCII mode data connection for file list
drwxr-xr-x 2 30344 1001 80 Oct 26 14:59 .
drwxr-xr-x 5 30344 1001 1024 Oct 26 14:59 ..
226 Transfer complete
Directory listing successful
Got reply 1 to the command 2
RMD /home/j/u/junonot/cgi-bin/test/
550 /home/j/u/junonot/cgi-bin/test/: Invalid argument
Got reply 4 to the command 64
Asking user:
Error deleting file 'test'. ("/home/j/u/junonot/cgi-bin/test/: Invalid argument")
Session upkeep