Searched high and low on the net, spoke to a University administration technicians, spoke to some local Apple technicians, but could not find anything substancial. I did, however, come across some well set out internal support documentation, with screen shots (helpful) from Cambridge University. This lead me to the Directory Access application in the Utilities folder, where a number of network services are ticked by default, including SMB. By simply un-ticking SMB service and connecting via afp://server-Address, all files without a prefix on the windows servers magically returned to their previous state.
These types of major but simple changes, like the missing Key Caps program should be put in "Whats new?" in the Apple Help. This was an OS 9 to OS X migration client; there are still thousands out there, that may have chosen to stay on OS 9...

