Hi, I could only reproduce this bug with sysvinit as init system. I think one could use runlevel (if it exists) to detect whether a real shutdown is running. Maybe something like the attached patch could fix the problem (not yet tested).
WM
diff --git a/debian/kexec-load.init.d b/debian/kexec-load.init.d
index 28306a7..f4de112 100644
--- a/debian/kexec-load.init.d
+++ b/debian/kexec-load.init.d
@@ -109,6 +109,9 @@ case "$1" in
exit 0
fi
fi
+ if [ -x /sbin/runlevel -a "$(runlevel | awk '{ print $2 }')" != "6" ]; then
+ exit 0
+ fi
do_stop
;;
*)
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