I have just about had it with intels ide drivers, for such a large company I have never used such a bad ide controller. This problem exists on windows XP as well, it is not unique to vista.
Drivers 7.0 and below - disables write cache forcefully on every drive in the pc including on other ide controllers massively reducing performance unless you happen to be using intel raid. So raid users wont notice this.
Drivers 7.8 - allows full write caching on drives on other controllers.
Drivers 8.0 - seem to be beta drivers, these drivers actually give proper write cache control can be set in device manager and can use power protected write cache like on all other ide controllers, problem is get the famous vista type problem of iastor timing out so I had to roll back to 7.8
Since only the system drive only really benefits from command queuing I am going to put my intel controller in ide mode so it uses microsoft drivers which at least work as they should and put my system drive on my jmicron controller which has given me no grief at all.
On a few other google hits I have seen others report as soon as they stopped using the intel controller or put in ide mode all these type of problems stop.
So the good news intel are doing driver development there is some recent beta drivers, the bad news they cant get it right after a number of years.