Running sysprep on a machine with multiple partitions..

Hello,

I have a Windows 2003 installation on a machine having 2 partitions.

C:\ is very small partition but it has loader files viz. ntldr,
ntdetect.com, boot.ini etc.
E:\ has the Windows 2003 installation viz. e:\windows, e:\documents
and settings etc.
D:\ is my CD ROM drive

I run sysprep on this machine with the command line "sysprep.exe -
quiet -reboot -reseal -mini". In sysprep.inf I specify all the
mandatory fields.

After sysprep finishes I observe the following

1. My E: drive becomes D:
2. My CD-ROM becomes E:
3. I get pop up for detection for new hardware for my network card.
If I select to install it says cannot find module to install.
4. It reports it can't find various files on E: drive as it has become
D
5. Opening any shortcuts on desktops gives file not found errors etc.

If I try the same scenario on a machine with only one partition with
Windows installed on C:, everything works fine.

I read the following KB which says "Sysprep can only be run on an
installation that resides in the C: partition. Sysprep does not
support creating images of computers that have multiple partitions."

http://support.microsoft.com/kb/830958/en-us

Is this indeed the case? If its true then I cannot really use sysprep
in the scenario I mention above.

Can anybody confirm?

Thanks.
-Prasad