Then let's try delayed startup as workaround for the mce (alarmd??) bug.
Keep alarmd disabled at boot.
Put this script uncompressed in /etc/init.d and make it executable ("chmod +x /etc/init.d/delayed-alarmd")
Activate it at boot ("update-rc.d delayed-alarmd start 99 2 3 4 5")

This startup script will start alarmd with a 1 minute delay, hopefully the boot process will have finished by then and it'll work just like when you did it by hand. If it doesn't work, we can try with a 2 minute delay (just edit the script and change "sleep 60" to "sleep 120")