This may be paranoid or superstitious, but I've noticed that booting Ubuntu often fails if there are USB devices plugged in at boot time. Since I've an external DVD drive, external hard disk, and a USB wireless dongle, this is quite a problem!
I've tried turning off USB support in the BIOS and that seems to cure it.
In fact the boot process seems faster and more reliable.
It doesn't seem affect Ubuntu's ability to access USB hardware at all.
Of course, in order to boot off a DVD, it needs to be turned it back on!