So even AHCI causes trouble for some, what a mess.
Try installing the 12.9 driver. The creator of this thread had a Z97 motherboard and it works for him. This should fix your problem and there is no performance loss. This is the best solution at this time in my opinion.
An alternative is to disable APM using crystal disk info. Go to Functions>Advanced Feature and make sure Auto AAM/APM Adaption is enabled. Then go to Functions>Advanced Feature>AAM/APM control and press disable once on every drive that you want to disable it on.