I can confirm that this isn't Ubuntu's fault, but the default setting of the HDD's firmware itself. I downloaded the Drive Feature Tool from Hitachi's website and used it to turn off APM and haven't had this problem since. I also disabled Acoustic Management whilst I was there, so now the drive is slightly noisier but performs better... both of these features were enabled by the manufacturer (Dell) by default. A few minutes of battery life for potential extra years of HDD life... a fair trade I think!
For those of you who don't own Hitach/IBM drives, there is the Ultimate Boot CD -
http://www.ultimatebootcd.com/ - that contains other manufacturer's utilities that do the same thing for their drives. You shouldn't have to change anything in the OS to fix this although you might need to if there is no utility for your particular HDD. I know some of those manufacturers have released firmware updates that fix this on their drives.
Regards,
Neil.