Unattended installation disorganizes program files location

I'm trying to get windows 2003 server x64 to install properly by supplying a winnt.sif file. With properly I mean that the program files just don't belong on the same partition as the OS is on. As this type od servre runs apps in 64bit and in 32bit modes, there are 2 program files locations, \Program Files\, And \Program Files (x86). This is the same with the x64 bit version of XP, so the winnt.sif files will be the same for either OS's. So I added the following entries into the file in the [unattended] section:

ProgramFilesDir = "D:\Program Files"

ProgramFilesDir(x86) = "D:\Program Files (x86)"

CommonFilesDir = "D:\Program Files\Common Files"

CommonFilesDir(x86) = "D:\Program Files (x86)\Common Files"

After the installation I end up with the following directories:

C:\Program Files (x86)\ not at all what I want!

C:\Program Files (x86) (x86) even less than what I want, and where would 2 (x86)'s come from?

D:\Program Files This at least is OK.

D:\Program Files (x86) This is OK too.

Does anyone know how I can get rid of the entries in C:\Program...... with using the winnt.sif file?

Thanks for your help.