Problems Keeping Conditional Build Tags when generating from the command prompt

I am attempting to generate various projects from the batch file using RH8. When I generate from the Robohelp interface the output is fine.

But when I use the batch file in a command prompt window, the conditional build tags are not applied in the finished output.

And during generation I recieve various errors such as, "Warning: No baggage file description" and a lot of "Template Error: cannot resolve macro" about 10 of the template errors per project.

Does anyone have any ideas why the conditional tags are not applying during the command prompt generation...? I followed the RH Guidebook to a properly write the command promtpts.