As I am continuing my efforts to improve Ubuntu boot time [1] I started noticing that bootchart [2] would list several processes twice and the boot logs would complain that all mountpoints were busy or had been mounted already.
A closer inspection of the logs reveals that indeed several scripts were being executed twice: the console setup, pulseaudio and the mountall daemon.
It turns out that upstart is executing any scripts in the subtree of /etc/init and thus also the obsolete scripts which I parked in /etc/init/bak, while the correct way to disable them is to either delete them or rename them to a different file suffix than .conf which, incidentally, also solved the problem.
Resources
[1] Speeding up Ubuntu 11.04 boot time
https://blog.georgovassilis.com/2011/05/03/speeding-up-ubuntu-11-04-boot-time/
[2] Bootchart
http://www.bootchart.org/
George's Techblog 