We believe that your issue has been closed by the upload of
Version 0.93.2-grml01 of initramfs-tools from Michael Prokop <mika@grml.org>.
The explanation is attached below

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Hash: SHA1

Format: 1.8
Date: Fri, 15 May 2009 17:40:28 +0200
Source: initramfs-tools
Binary: initramfs-tools
Architecture: source all
Version: 0.93.2-grml01
Distribution: unstable
Urgency: low
Maintainer: Debian kernel team <debian-kernel@lists.debian.org>
Changed-By: Michael Prokop <mika@grml.org>
Description: 
 initramfs-tools - tools for generating an initramfs
Changes: 
 initramfs-tools (0.93.2-grml01) unstable; urgency=low
 .
   * Get rid of the "modprobe: FATAL: Could not load
     /lib/..../modules.dep: No such file or directory" error message
     via touching modules.dep. [Closes: issue639]
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 2051900c1e16882ee85d6c43aee22e2190020327 522 initramfs-tools_0.93.2-grml01.diff.gz
 dbafb9666dce747632631bfbd61b15d7e700efd0 74532 initramfs-tools_0.93.2-grml01_all.deb
Checksums-Sha256: 
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Files: 
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Fixed by attached patch.

Related to http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=508178 - the 
reasons seems to be modprobe of live-initramfs's scripts/live-premount/modules.

In the daily-snapshot ISOs you'll notice

"modprobe: FATAL: Could not load /lib/..../modules.dep: No such file or 
directory"

in the initramfs part of booting. We have to investigate on that.