This is fixed in newer versions.
The issue you ran into is because Ubuntu is using ucf to maintain grubs
menu.lst...
Please read all about it here:
http://faiwiki.informatik.uni-koeln.de/index.php/FAIUbuntuGrubProblems
Thx,
\sh
** Changed in: fai (Ubuntu)
Status: New => Won't Fix
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fai-server doesn't install GRUB
https://bugs.launchpad.net/bugs/274857
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