command line build problem

We have a large help project I'm migrating to RoboHelp 6 (nearly 3000 topics, 12 chms plus a master file). We generate using a script that calls the command-line option. One of the projects fails during command line processing, even though I can build it from within the GUI without fail. When I run the command line command, this is the message that is returned:

"D:\quartus\robohelp\subs\reference>"d:\Adobe\RoboHelp 6.0\RoboHTML\RHCL.exe" reference.xpj
Adobe (R) RoboHelp Project Command Line Compiler version 6.00.099
Copyright (C) 2006 Adobe Macromedia Software LLC. All rights reserved.

Project: D:\quartus\robohelp\subs\reference\reference.xpj
Layout: Microsoft HTML Help.
Output: D:\quartus\robohelp\reference.chm.

Scanning project for compilation....
Error: Failed to scan all the project files. Please use RoboHelp to recover the project.
Unexpected Error: Failed to prepare single source data for RHCL. Please try to compile it in RoboHTML."

If I open the project in the GUI and compile it, then compile from the command line, it works fine. But if I clear the directory, run the NGCMD.exe command and get the files out and run the RHCL.exe, I get the same error message.

Thanks