If Windows detects a certain number of disk errors, it assumes that DMA may be the problem and it automatically sets the drive to PIO mode (without telling you).
Sometimes, even though you set it back to DMA mode, Windows will continue to use PIO mode. The only way to fix this problem is to delete the controller, then re-boot and let Windows will reinstall it. Once the controller is re-installed, you can set the drive back to DMA mode. (If you need to do this, delete the controller, not the drive).