Some general considerations are below.
1.
Please check if SATA and PCIe volatges are applied : according to footnote of Table 2-21
(Recommended connections for unused analog interfaces) of the Hardware Development Guide,
linked below , SATA and PCIe supplies must remain powered if boundary scan test needs to be done.
http://cache.freescale.com/files/32bit/doc/user_guide/IMX6DQ6SDLHDG.pdf
2.
JTAG_MOD (SJC_MOD) should be pulled up (to NVCC_JTAG) for Boundary Scan Mode.
3.
Please pay attention on COMPLIANCE_PATTERNS of the BSDL file.
attribute COMPLIANCE_PATTERNS of MX6S: entity is
"(TEST_MODE, JTAG_MOD, POR_B) (011)";
Check if :
TEST_MODE is LOW ;
JTAG_MOD is HIGH ;
POR_B is HIGH.
Regards,
Yuri.