This bug was fixed in the package ltsp - 5.1.75-0ubuntu1

---------------
ltsp (5.1.75-0ubuntu1) karmic; urgency=low

  * new upstream version (5.1.75)
   * Use Debian's scripts when possible (LP: #380072)
   * Support per session Xauthority
   * Don't hardcode opt/ltsp in ltsp-update-kernels (LP: #294643)
   * Set LANGUAGE to the user's locale for localapps
   * Improve ltsp_nbd with better defaults for buggy networks.

 -- Stephane Graber <[email protected]>   Wed, 03 Jun 2009 17:28:44
-0400

** Changed in: ltsp (Ubuntu)
       Status: Fix Committed => Fix Released

-- 
ltsp-update-kernels removes all kernels from tftpboot dir if base is not 
/opt/ltsp
https://bugs.launchpad.net/bugs/294643
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