Hello,
1.
from just built Linux :
root@imx6qsabresd:~# uname -a
Linux imx6qsabresd 4.1.15-1.1.1+gd5d7c02 #1 SMP PREEMPT Tue May 17 16:33:36 OMST 2016 armv7l GNU/Linux
2.
Looks like really eMMC located kernel and filesystem are used in the case.
Please check carefully Your boot settings and U-boot environment.
Difference between eMMC and SD is just port number.
Regards,
Yuri.