Slow boot on SATA III

Hello guys,

I have a problem with the current Netrunner version. I recognized a long boottime on my pc. This happens after the grub bootloader. My display is going to sleep mode and nothing is happen for about 10-20 seconds. After that time, my pc is doing the normal stuff, like booting the system and showing the login screen.
This happens only on my old SSD and the new one, when they are pluged in the SATA III interface.
The history is:
At first I had installed Windows 8.1 on my first SSD. After that I installed Netrunner on a separate partition on my HDD (SATA III Interface) and all was fine. I was really excited about netrunner so I want to make it to my primary OS. For that, I took a second small SSD (60GB) and installed netrunner on it. This was the first time I noticed the above mentioned slow boot time, that actually needs more time, than the installation on HDD.
After a couple of days I bought the Samsung 850 Evo with 120GB and I have cloned Windows 8.1 to this SSD. All worked fine. Than I installed on the same SSD netrunner 17 and all was fine too. While the installation the HDD was not connected (so the SSD netrunner does not recognizes the old HDD netrunner installation).
So long so good. I was looking at Samsungs magician software that says, my SSD is only at the SATA II port, so I checked it. The result is, that I have forgotten to switch the new Samsung SSD to the SATA III port. After switching to correct port, I’m getting the above issue with slow boot time, while netrunner boots very slow.

Because the error does not show, when connection on the SATA II port and is present on two different SSDs I don’t think this will be hardware error. With the Windows I don’t have any issues.

Do you have ideas, how I can fix this issue?

Ah I forgot to mention my pc specs:
i5-2500k @ 4.0 Ghz
Nvidia 560 TI
Samsung 850 EVO 120 GB
Thosiba 4 TB HDD