I am setting up S900 with Naza M V2 using  a Futaba 8J radio transmitter. During the motor test, I only get responses from motors 3-4-5-6 and they are not in the correct order (but are spinning in right direction). If I change multicopter configuration from a Hex V to an octocopter, all the motors will respond (even 1/2), but they too do not match up to their actual motor numbers. So I know that motors 1/2 work. 6 of the 8 octocopter motors (3-8) will respond.

What am  I doing wrong? Is this a transmitter issue? Any help would be appreciated!!!

For you first question, please ensure if the connection of M1-M8 is correct or not. Or you can shoot a picture of it for further check. If the connection is correct, please try to flash the firmware. Please keep us updated, thanks.