It caused my HDD to spind down every other reboot (not always, after a longer Windows session), and on shut down it would preform an emergency lock (like if I unpowered the HDD suddenly). I never found an answer what exactly was going on.
I know IAA was the problem. Now I use Ultra ATA Storage Driver (which is an old version of IAA). I don't know if it replaces MS IDE drivers, I think it does. My system if Intel D850MV mobo and IBM GXP60 drive.
On newer systems I don't think there would be any problems, so I'd use it. It has some nice control options such as optimizing your drive for minimum noise, it does show what mode it is running in and you can change it. Plus a lot of info like your HDD firmware version.