E6540 slow SSD performance

I installed a 250GB Samsung EVO 850 (non Pro) mSata SSD in a Dell Latitude E6540.

Fresh Windows 7 Enterprise 64-bit install

Sophos  SafeGuard 5.50 full disk encryption

16GB RAM

RAID On mode set in BIOS, but no RAID volume sets

A16 BIOS version

Intel QM87 LPC Controller driver version 9.4.0.1023

I am running disk benchmarks and getting about 40% of the throughput of the specs.  ATTO, Samsung Magician, and AS SSD all reporting similar results.  Appears to be running at SATA II speed 3Gbps instead of 6Gbps.

E6540 uses an Intel QM87 chipset, which runs 6 SATA Ports @3Gbps and 4 SATA ports @6Gbps

Intel Rapid Store Technology reporting 6Gbps SATA Transfer rate for the SSD.

Samsung Magician is unable to detect the SATA interface.

AHCI is not an option, as it breaks SOPHOS and the drive will not boot, RAID I believe delivers the same performance as AHCI.

I disabled 2 of the SATA ports in the BIOS, only detects the 2 drives on SATA-0 (HDD)  and SATA-4 (SSD).

The WiGig adapter has been disabled.

WLAN, WWAN, and Bluetooth are enabled.

How can I check the number of SATA ports being used? or enabled?  I am assuming the SATA ports are running @3Gbps, SATA II mode.