Before posting, please read how to report bug or request support effectively.
Bug reports without an attached log file are usually useless.
I'm sorry for late answer. In GUI you are removing different files than in console. Can you post a log files showing removal of the same file?
Searching for host...
Host does not exist
batch on
confirm off
Searching for host...
Connecting to host...
Authenticating...
Using username "****".
Authenticating with pre-entered password.
Authenticated.
Starting the session...
Reading remote directory...
Session started.
Active session: [1] ****@stageftp.fiftyone.com
/outbox/orders
Error deleting file '/outbox/orders/2011-01-24-14-55-34-PO-E4X000000495717.xml.a
sc'.
General failure (server should provide error description).
Error code: 4
Error message from server (en): error deleting file
Request code: 13
(A)bort, (R)etry, (S)kip, Ski(p) all: Abort
drw-rw-rw- 3 user group 0 Jan 31 11:22:41 2011 .
-rw-rw-rw- 1 user group 6500 Jan 28 21:38:22 2011 2011-01-24-14-55
-34-PO-E4X000000495717.xml.asc
drw-rw-rw- 3 user group 0 Jan 25 23:27:44 2011 Archive
-rw-rw-rw- 1 user group 6500 Jan 28 10:23:27 2011 _2011-01-24-14-5
5-34-PO-E4X000000495717.xml.asc
winscp>
c:\WinSCP\WinSCP.exe winscp.exe /console /script=fcom.txt /log="C:\winscp.log"
# Automatically answer all prompts negatively not to stall
# the script on errors
option batch on
# Disable overwrite confirmations that conflict with the previous
option confirm off
# Connect using a password
# open user:password@example.com
# Connect:
open sftp://User:Password@stageftp.fiftyone.com
# Change remote directory
cd /outbox/orders
rm /outbox/orders/2011-01-24-14-55-34-PO-E4X000000495717.xml.asc
dir
#close
# Disconnect