Also, I am making changes to my config file and even renaming it to try to force that the cmd line takes precedence but it still returns it is using the same config file in my appdata folder - even after I rename it.

Tried shutting down and restarting the GUI. How do I stop it using the config file?  

I have installed client tools and successfully set up a site and transferred a file via the GUI Pragma Fortress FX.  I can see my file in the navigation pane and the admin has confirmed transfer.  I am using SSH2 certificates with no password and a specified non-default port eg 10xxx. 

I need to automate the secure copy and therefore need to get it working via command line.  Source  server is Win 2012.

Trying these commands:
C:\Program files\Pragma\Clients\scp user@server:/share/folder Filename 
returns secure connection refused

C:\Program files\Pragma\Clients\scp -v user@server:/share/folder Filename
returns
EXecuting host <server in cmd line>
User <user in cmd line>
Command scp -v -f /share/folder
Pragma Fortress SSH 5.0 SSH Protocol 2.0
Reading configuration data inC:\Users\xxxx\APpData\Roaming\config
Connect Failed 0
Secure connection refused

C:\Program files\Pragma\Clients\ssh -v user@server:/share/folder
returns
Pragma Fortress SSH 5.0 SSH Protocol 2.0
Reading configuration data inC:\Users\xxxx\APpData\Roaming\config
Connect Failed 11001
Secure connection refused

Configuration file is:
IdentityFile2 D:\Pragma\ssh2_rsa.pub
RSAAuthentication Yes
PubKeyAuthentication Yes
PasswordAUthentication No
Port 10xxx

I tried it without the config file first but no luck.

Any guidance much appreciated.  Thanks in anticipation.