Multi Installation SH3Commander woes!

[kevtherev]

I have been working on the following problem now for 2 days and cannot seem to get any further with it, could someone out there please help.
Multi installations of SH3 are as follows:-
(a) D:\SilentHunterIII + 1.4patch + JSGME (new unmodded game installation)
(b) D:\(copy of (a) and renamed) GreyWolves + MultiSH3.exe for save file rename to GWX
(c) D:\(copy of (a) and renamed) NYGM + MultiSH3.exe for save file rename to NYG
Mods were then installed as necessary for the different installations.
After running each one the following folders appeared in My Documents folder, +GWX, +SH3 and +NYG all with related data etc.
So far so good ?
I then installed seperate copies of SH3Commander in:-
(a) C:\Programme, for GWX together with the GWX Commander cfg. files.
The Target for this shortcut was then changed from "C:\Programme\SH3 Commander\SH3Cmdr.exe"to:-
"C:\Programme\SH3 Commander\SH3Cmdr.exe" /1:"D:\GreyWolves"
(b) "C:\Program Files, for SilentHunterIII (no change to shortcut target).
(c) "C:\PROGRAMS, for NYGM together with NYGM 2.2 Commander cfg. files.
The Target for this shortcut was then changed from "C:\PROGRAMS\SH3Commander\SH3Cmdr.exe" to:- "C:\PROGRAMS\SH3Commander\SH3Cmdr.exe" /1:"D:\NYGM"
As said, all three installations of the game were run, however when I try to access GreyWolves or NYGM through their repective Commander shortcuts I am only accessed to the STOCK game version.
Please, please, any help on this one, I think that it must lay with the shortcut target naming.
Please note that I am not by any means a PC wizard, I am English but my system is German (as I live here) but I think ?? that I have done everything as should be done.
On the shortcut a mouse right click opens menu with 'Eigenshaft' which when left mouse clicked opens window with 'Verknüpfung' (link) in which is 'Ziel:' (target). This is the line of script which I am changing.
SH3 Commander version is v2.7.0.130