I guess you checked the wrong doc:rolleyes:
http://www.supermicro.com/manuals/motherboard/C202_C204/MNL-1270.pdf
page 1-10, the 1st/2nd/3rd slot comes out of CPU, the 4th slot comes out of PCH, no switch involved. and BTW the board has no x1 slot.
I have similar problem, same Supermicro X9SCM-F, same firmware version 2.0a, same three M1015 cross flashed to IT mode, same ESXi 5u1, same "mpt2sas2: _base_wait_for_doorbell_int: failed due to timeout count(10000)" message, same working fine out of ESXi, but I'm using Debian 7 instead of...