7i95T not seeing encoders or outputing step signals

1. Encoders do not increment counters - hm2/hm2_7i95.0:     IO Pin 018 (TB1-01/TB1-09): Muxed Encoder #0, pin Muxed A (Input)
hm2/hm2_7i95.0:     IO Pin 019 (TB1-04/TB1-12): Muxed Encoder #0, pin Muxed B (Input)
I have tried all encoder inputs using a stepper motor with attached encoder in differential mode. See signals clearly at TB1

2. Steps in Axis UI show movements from jogging in registers but do not show up on output pins TB3 or TB4 . 
Tech at Mesa sent me a code snippet that did produce very slow signals at TB3 but the commands are not clear to me and I don't think they help debug.

From startup: 
Machine configuration directory is '/home/bill/linuxcnc/configs/7i95t_xyz'
Machine configuration file is '7i95t_xyz.ini'
Starting LinuxCNC...
linuxcnc TPMOD=tpmod HOMEMOD=homemod EMCMOT=motmod
Note: Using POSIX realtime
Found file(REL): ./main.hal
hm2: loading Mesa HostMot2 driver version 0.15
hm2_eth: loading Mesa AnyIO HostMot2 ethernet driver version 0.2
hm2_eth: 192.168.1.121: INFO: Hardware address (MAC): 00:60:1b:15:82:8b
hm2_eth: discovered 7I95T Thanks for any help. I don't want to pull my hair out, but is is getting close.... 
Bill Witt

The fact that the stepgen outputs work with  the test program
indicates that the hardware is likely OK.

The test program is this:

 

Which will slowly toggle all step/dir outputs on any Mesa Ethernet FPGA card.
You may need to edit the file to change the IP address or select a different rate.
The default rate is quite slow to allow a DVM settling time to read both low and
high voltage states.

Did you try jogging in either direction with LinuxCNC to see if the DIR state changes?

The hal/ini file you sent had quite short step times (1000 ns) so could be a reason
for no motion. (Starting step times should be at least double the drives minimum timing)

If nothing else works, Mesa can issue a RMA for analysis/repair/replacement of the card
but the symptoms are very odd and don't  look at all like typical hardware issues.