Command line compiler (rhcl.exe) adds on rogue full pathways into [Merge Files] of .hhp

I'm using RH 9 and generating chm outputs on my Win 7 64-bit computer.
I have a core chm help file and several sub chm helps that get merged into it.
I have a batch file that regularly compiles our help files locally and then copies them into a common local directory. It then copies them up to a mapped network drive where they are picked up by the nightly build of our installer.
The problem I have, is that the command line compiler (rhcl.exe) is adding on a full pathway for all the sub helps listed in the [Merge Files] section of the core help's .hhp file, causing these problems:
1) First of all, the pathways are wrong. The pathway it puts on is from the location of my .xpj file of my core help project. The output directory for the compiler is actually sending all the helps to a different local directory.
2) These need to be relative, and should not have full pathways. The full pathways make it so that when I click on a subhelp TOC entry that subhelp's topic opens up in an entirely different window instead of merged into the core help's window. (See #13 on Peter's helpful site here about the problem with absolute paths: http://www.grainge.org/pages/authoring/rh9/using_rh9.htm)
Here' what I want it to look like (the good):
[MERGE FILES]
pcdmisportable.chm
pcdmistutor.chm
pcdmisvision.chm
pcdmislaser.chm
pcdmiscmm.chm
pcdmisUJB.chm
pcdbasic.chm
toolkitmodulesvwmp.chm
pcdmisdci.chm
toolkitmodules.chm
pcdmisnc.chm
pcdmisip.chm
toolkitmodulesblade.chm
pcdmisregistry.chm
pcdmisfixturing.chm
Here's what it looked like after the command line compile (the bad and the ugly):
[MERGE FILES]
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisportable.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmistutor.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisvision.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmislaser.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmiscmm.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisUJB.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdbasic.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\toolkitmodulesvwmp.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisdci.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\toolkitmodules.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisnc.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisip.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\toolkitmodulesblade.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisregistry.chm
d:\hg\pcdmisqa\pcdlrn\help\corehelp\pcdmisfixturing.chm
I've done the following ....
I've checked my .xpj file and they have relative paths only.
I've deleted my .cpd file.
I've removed chm references from my rhbag.apj.
... and the hhp file still gets modified with pathways to my core project
directory tacked on:
It's strange; because if I compile without the command line, by opening the project and running the generation inside of RH, I don't get the problem where it re-writes the [Merge Files] section with the pathnames.
Any ideas on where are these rogue full pathways coming from and how I can fix it? Or is it just a bug with the command line version of the compiler that Adobe will need to fix?

I don't use command line generation but to the best of my knowledge, this has not been fixed.
Please follow this link.
http://www.Adobe.com/cfusion/mmform/index.cfm?name=wishform&product=38
See www.grainge.org for RoboHelp and Authoring tips
@petergrainge

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Command line compiler (rhcl.exe) adds on rogue full pathways into [Merge Files] of .hhp

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