Pygrub doesn't detect the grub2 config file when it's on a separate /boot partition. This should fix it.
--- /a/usr/bin/pygrub 2010-03-04 12:32:36.000000000 +0000
+++ /b/usr/bin/pygrub 2010-03-05 08:16:57.000000000 +0000 @@ -383,7 +383,7 @@ ["/boot/grub/menu.lst", "/boot/grub/grub.conf", "/grub/menu.lst", "/grub/grub.conf"]) + \
map(lambda x: (x,grub.GrubConf.Grub2ConfigFile), - ["/boot/grub/grub.cfg"]) + ["/boot/grub/grub.cfg","/grub/grub.cfg"])
if not fs: # set the config file and parse it
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