OK, so I won't do any mod on this as long as warranty is provided for my board.
Since ASUS drivers work as intended, even the normal RST drivers (no enterprise), I think I will download my drivers from ASUS now. The clicking noise is still there, but I will buy some SATA-controller in the near future, so that's no problem anymore, too.
So I only have to wait about what the tech-dept. will answer about the PCIe 3.0 issue, that's fine. Let's wait ... :-)
And before I forget it: What's "Intel Management Engine Interface" (Intel MEI) needed for?
But who should I give credit now for the "solution" of all these issues? You helped both, but I only can give one of you the credits. Diego_Intel, would you mind if I give "Ziad Aghar" the credits? This user has less points than you. Probably he / she could need them more.
Sincerely
IDDQD
EDIT: Sorry guys, but I found another issue, but I think that's peanuts for you guys. (i hope so!)
After installing Win8 from scratch (like I always do), I installed the drivers first (mentioned above). The system shut down correctly for a while, but since a few days, the system shuts down, but the computer doesn't loose power. Then you hear some clicking noise, if the system would access and spin-up the HDDs again (on SATA-2 obviously, since on SATA-3 there are only SSDs). After spinning them up, the system looses power and shuts down as it should. For the whole time, the screen is black (no signal).
short:
shutdown command -> Windows tells you about shutdown bla bla -> screen goes black -> some clicking noise -> HDDs seem to spin up -> system goes offline like it should
how it should be / how it was:
shutdown command -> Windows tells you about shutdown bla bla -> screen goes black -> system is shut down / off!
There is no entry in Windows or anything else what could lead me to a solution. There are no errors with startup or shutdown or anything else. I did not change any drivers, which could lead to this and I did not install anything else. It happened from one day to another.