Mesa 7i76eu Encoder Questions

I have a 7i76eu that I am using on a new lathe conversion. I must have something wrong with firmware or something on the 7i76eu. The configuration is set up with 3 encoders is what it says. I only have one encoder connected to the 7i76 on tb3. It is configured as single ended jumpers w11 w12 and w16 all set to the left position (up in my case). When I look at the inputs in halshow the A signal is showing up as the A signal on encoder 0, the B signal is showing up as the A signal on encoder 1 and the index signal is showing up as the A signal on encoder 2.

What do I have incorrect here. My mesa setup is a 7i76eu with just a 7i73 pendant smart serial card. I have one spindle drive, one encoder that I am using on the 7i76 two steppers and several io.

I downloaded the firmware pack from Mesa. I installed one that just had the 7i76in the name but no other cards. Which firmware should I use in this case? 

Not sure if this is a config or a firmware mismatch issue. Any help would be appreciated.

If you don't have an added parallel daughtercard, you should normally not change the
installed firmware.

The default 7I76E firmware is 7i76eud.bin, to re-install:

mesaflash --device 7i76eu --addr [card_ip_address] --write 7i76eud.bin --reload

where [card_ip_address]  is either 192.168.1.121 or 10.10.10.10 depending on how you
have the card setup.