I have a Supermicro motherboard X8ST3-F in a Supermicro 4U Case 846E1-R900B. I have the LSI 1068E in I/T mode to connect to the 846E1-R900B built in backplane. I am using a reverse break out cable to go from the 4 discreet SATA (0,1,2,3 off of the LSI 1068E) to SSF-8087 to connect to the backplane. I am unable to see any of my hard drive when I connect them through the backplane.
It depends on what type of Mini-Ipass to 4 SATA break out cable you have, but make sure the cable is support cross-over cable. The part number is CBL-0116L, you may order from Super Micro RMA parts department at 1-408-503-8000 press 3 or email to: rma@supermicro.com