If you need to switch SATA modes after operating system has been installed is not supported by the Intel technical department because you will need to reinstall your operating system and set correct SATA mode through BIOS setup.
Below I have found a possible fix via Windows registry.
Sadly that link is dead. It has been mentioned in several articles online but sadly they all point to the dead link and don't re-post the contents. And MSI doesn't seem forthcoming in simply calling their forums, forums. As it is hidden somewhere in their maze of a site. I know intel says they do not provide support. However if there is one thing every techie knows, there is a fix, just that it doesn't always work or is extremely complicated and so the company, whether it be Intel, AMD, Microsoft and so on, do not want to expend their tech support dealing with the possible hundreds of thousands of possibilities of different configurations and different systems. Sadly due to the litigious of our country (I am in the US), companies don't even want to dare mention something that can fix something but they have to put up a disclaimer which someone will sue them for missing a dotted i or a crossed t in the disclaimer. Disappointing. I hope there is a solution out there.
As I said the problem is that Intel sells the z68 chipset with 2x4 SATA ports but has only a 6 port SATA ahci driver with their supposed native inf chipset drivers. You have to turn to the RST disk and use a driver that doesn't even say it supports the 2x4, 6 or anything related to Z68. It just makes things so much more confusing and harder to solve. As I said the ahci they have doesn't match their configuration, unless the 2x4 is simply 6 port, but then is it c01 or c02 and so on. Like being handed to guns while you are blindfolded and told one has a round in the chamber and the other one shouldn't have a round but we can't promise and you have to pull one of them.