Additional info:
At first I was using ONLY the on-board SATA (Ibex Peak).
There, I also mentioned Problems.
Especially, I had the same effect as on the PERC with 2 HD with capacity 1TB and 1.5TB (Seagate Constellation 1TB and WD green 1.5TB)
The drives itself seem to be okay.
The reason of purchasing the PERC was to get rid of These Problems as somebody told me, the Ibex Peak Controller is the reason for the Errors and is unsupported.
The Mainboard is a GA-H55M-USB3 with a i5-680 CPU and vt-d enabled.
Edit:
The ESXi itself is on a USB-Stick.